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commit/galaxy-central: carlfeberhard: History panel: allow anon use of dataset search
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5830078f639c/ Changeset: 5830078f639c User: carlfeberhard Date: 2013-12-03 21:13:17 Summary: History panel: allow anon use of dataset search Affected #: 5 files diff -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 -r 5830078f639cd0b145ca3975f9c621c3d3b69cf1 static/scripts/packed/templates/compiled/history-templates.js --- a/static/scripts/packed/templates/compiled/history-templates.js +++ b/static/scripts/packed/templates/compiled/history-templates.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-body"]=b(function(g,r,p,k,z){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);z=z||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(D,C){var A="",B;A+='\n <div class="dataset-summary">\n ';if(B=p.body){B=B.call(D,{hash:{},data:C})}else{B=D.body;B=typeof 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Click 'Get Data' on the left pane to start"}q+='<div class="history-controls">\n\n <div class="history-title">\n \n ';i=p["if"].call(r,r.name,{hash:{},inverse:o.noop,fn:o.program(1,n,u),data:u});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=p["if"].call(r,r.nice_size,{hash:{},inverse:o.noop,fn:o.program(4,l,u),data:u});if(i||i===0){q+=i}q+='\n\n <div class="history-secondary-actions"></div>\n </div>\n\n <div class="message-container">\n ';i=p["if"].call(r,r.message,{hash:{},inverse:o.noop,fn:o.program(6,j,u),data:u});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:o.noop,fn:o.program(8,h,u),data:u};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+=".\n ";f={hash:{},inverse:o.noop,fn:o.program(10,t,u),data:u};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='.\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:o.noop,fn:o.program(12,s,u),data:u};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+="\n </div>";return q})})();(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(h,s,q,l,w){this.compilerInfo=[4,">= 1.0.0"];q=this.merge(q,h.helpers);w=w||{};var r="",i,f,p=this,e="function",c=q.blockHelperMissing,d=this.escapeExpression;function o(B,A){var x="",z,y;x+='\n <div class="history-name" title="';y={hash:{},inverse:p.noop,fn:p.program(2,n,A),data:A};if(z=q.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!q.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+='">\n ';if(z=q.name){z=z.call(B,{hash:{},data:A})}else{z=B.name;z=typeof z===e?z.apply(B):z}x+=d(z)+"\n </div>\n ";return x}function n(y,x){return"Click to rename history"}function m(A,z){var x="",y;x+='\n <div class="history-size">';if(y=q.nice_size){y=y.call(A,{hash:{},data:z})}else{y=A.nice_size;y=typeof y===e?y.apply(A):y}x+=d(y)+"</div>\n ";return x}function k(B,A){var x="",z,y;x+='\n <div class="warningmessagesmall"><strong>\n ';y={hash:{},inverse:p.noop,fn:p.program(7,j,A),data:A};if(z=q.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!q.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </strong></div>\n ";return x}function j(y,x){return"You are currently viewing a deleted history!"}function g(A,z){var x="",y;x+='\n \n <div class="';if(y=q.status){y=y.call(A,{hash:{},data:z})}else{y=A.status;y=typeof y===e?y.apply(A):y}x+=d(y)+'message">';if(y=q.message){y=y.call(A,{hash:{},data:z})}else{y=A.message;y=typeof y===e?y.apply(A):y}x+=d(y)+"</div>\n ";return x}function v(y,x){return"You are over your disk quota"}function u(y,x){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function t(y,x){return"Your history is empty. Click 'Get Data' on the left pane to start"}r+='<div class="history-controls">\n\n <div class="history-title">\n ';i=q["if"].call(s,s.name,{hash:{},inverse:p.noop,fn:p.program(1,o,w),data:w});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=q["if"].call(s,s.nice_size,{hash:{},inverse:p.noop,fn:p.program(4,m,w),data:w});if(i||i===0){r+=i}r+='\n\n <div class="history-secondary-actions"></div>\n </div>\n\n ';i=q["if"].call(s,s.deleted,{hash:{},inverse:p.noop,fn:p.program(6,k,w),data:w});if(i||i===0){r+=i}r+='\n\n <div class="message-container">\n ';i=q["if"].call(s,s.message,{hash:{},inverse:p.noop,fn:p.program(9,g,w),data:w});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:p.noop,fn:p.program(11,v,w),data:w};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+=".\n ";f={hash:{},inverse:p.noop,fn:p.program(13,u,w),data:w};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='.\n </div>\n \n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:p.noop,fn:p.program(15,t,w),data:w};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+="\n </div>";return r})})(); \ No newline at end of file diff -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 -r 5830078f639cd0b145ca3975f9c621c3d3b69cf1 static/scripts/packed/templates/compiled/template-history-historyPanel-anon.js --- a/static/scripts/packed/templates/compiled/template-history-historyPanel-anon.js +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel-anon.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel-anon"]=b(function(g,r,p,k,u){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);u=u||{};var q="",i,f,o=this,e="function",c=p.blockHelperMissing,d=this.escapeExpression;function n(z,y){var v="",x,w;v+='\n <div class="history-name" title="';w={hash:{},inverse:o.noop,fn:o.program(2,m,y),data:y};if(x=p.local){x=x.call(z,w)}else{x=z.local;x=typeof x===e?x.apply(z):x}if(!p.local){x=c.call(z,x,w)}if(x||x===0){v+=x}v+='">\n ';if(x=p.name){x=x.call(z,{hash:{},data:y})}else{x=z.name;x=typeof x===e?x.apply(z):x}v+=d(x)+"\n </div>\n ";return v}function m(w,v){return"You must be logged in to edit your history name"}function l(y,x){var v="",w;v+='\n <div class="history-size">';if(w=p.nice_size){w=w.call(y,{hash:{},data:x})}else{w=y.nice_size;w=typeof w===e?w.apply(y):w}v+=d(w)+"</div>\n ";return v}function j(y,x){var v="",w;v+='\n \n <div class="';if(w=p.status){w=w.call(y,{hash:{},data:x})}else{w=y.status;w=typeof w===e?w.apply(y):w}v+=d(w)+'message">';if(w=p.message){w=w.call(y,{hash:{},data:x})}else{w=y.message;w=typeof w===e?w.apply(y):w}v+=d(w)+"</div>\n ";return v}function h(w,v){return"You are over your disk quota"}function t(w,v){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function s(w,v){return"Your history is empty. Click 'Get Data' on the left pane to start"}q+='<div class="history-controls">\n\n <div class="history-title">\n \n ';i=p["if"].call(r,r.name,{hash:{},inverse:o.noop,fn:o.program(1,n,u),data:u});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=p["if"].call(r,r.nice_size,{hash:{},inverse:o.noop,fn:o.program(4,l,u),data:u});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="message-container">\n ';i=p["if"].call(r,r.message,{hash:{},inverse:o.noop,fn:o.program(6,j,u),data:u});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:o.noop,fn:o.program(8,h,u),data:u};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+=".\n ";f={hash:{},inverse:o.noop,fn:o.program(10,t,u),data:u};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='.\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:o.noop,fn:o.program(12,s,u),data:u};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+="\n </div>";return q})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel-anon"]=b(function(g,r,p,k,u){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);u=u||{};var q="",i,f,o=this,e="function",c=p.blockHelperMissing,d=this.escapeExpression;function n(z,y){var v="",x,w;v+='\n <div class="history-name" title="';w={hash:{},inverse:o.noop,fn:o.program(2,m,y),data:y};if(x=p.local){x=x.call(z,w)}else{x=z.local;x=typeof x===e?x.apply(z):x}if(!p.local){x=c.call(z,x,w)}if(x||x===0){v+=x}v+='">\n ';if(x=p.name){x=x.call(z,{hash:{},data:y})}else{x=z.name;x=typeof x===e?x.apply(z):x}v+=d(x)+"\n </div>\n ";return v}function m(w,v){return"You must be logged in to edit your history name"}function l(y,x){var v="",w;v+='\n <div class="history-size">';if(w=p.nice_size){w=w.call(y,{hash:{},data:x})}else{w=y.nice_size;w=typeof w===e?w.apply(y):w}v+=d(w)+"</div>\n ";return v}function j(y,x){var v="",w;v+='\n \n <div class="';if(w=p.status){w=w.call(y,{hash:{},data:x})}else{w=y.status;w=typeof w===e?w.apply(y):w}v+=d(w)+'message">';if(w=p.message){w=w.call(y,{hash:{},data:x})}else{w=y.message;w=typeof w===e?w.apply(y):w}v+=d(w)+"</div>\n ";return v}function h(w,v){return"You are over your disk quota"}function t(w,v){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function s(w,v){return"Your history is empty. Click 'Get Data' on the left pane to start"}q+='<div class="history-controls">\n\n <div class="history-title">\n \n ';i=p["if"].call(r,r.name,{hash:{},inverse:o.noop,fn:o.program(1,n,u),data:u});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=p["if"].call(r,r.nice_size,{hash:{},inverse:o.noop,fn:o.program(4,l,u),data:u});if(i||i===0){q+=i}q+='\n\n <div class="history-secondary-actions"></div>\n </div>\n\n <div class="message-container">\n ';i=p["if"].call(r,r.message,{hash:{},inverse:o.noop,fn:o.program(6,j,u),data:u});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:o.noop,fn:o.program(8,h,u),data:u};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+=".\n ";f={hash:{},inverse:o.noop,fn:o.program(10,t,u),data:u};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='.\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:o.noop,fn:o.program(12,s,u),data:u};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+="\n </div>";return q})})(); \ No newline at end of file diff -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 -r 5830078f639cd0b145ca3975f9c621c3d3b69cf1 static/scripts/templates/compiled/history-templates.js --- a/static/scripts/templates/compiled/history-templates.js +++ b/static/scripts/templates/compiled/history-templates.js @@ -383,7 +383,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"message-container\">\n "; + buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n <div class=\"message-container\">\n "; stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; diff -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 -r 5830078f639cd0b145ca3975f9c621c3d3b69cf1 static/scripts/templates/compiled/template-history-historyPanel-anon.js --- a/static/scripts/templates/compiled/template-history-historyPanel-anon.js +++ b/static/scripts/templates/compiled/template-history-historyPanel-anon.js @@ -79,7 +79,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"message-container\">\n "; + buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n <div class=\"message-container\">\n "; stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; diff -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 -r 5830078f639cd0b145ca3975f9c621c3d3b69cf1 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -69,6 +69,8 @@ {{#if nice_size }} <div class="history-size">{{nice_size}}</div> {{/if}} + + <div class="history-secondary-actions"></div></div><div class="message-container"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History panel: allow searching datasets: name, tags, annotation, dbkey, file_ext, blurb, and info will be searched when enter is pressed in the search field, include whitespace by enclosing search term in double quotes, allow specifying which field to search by using the idiom 'field=term' where field is any of the previous field names (or more user-centric aliases: database for dbkey, etc.), (GUI filters as an alternate means to accomplish field specif
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a6044ab1ffe7/ Changeset: a6044ab1ffe7 User: carlfeberhard Date: 2013-12-03 21:03:32 Summary: History panel: allow searching datasets: name, tags, annotation, dbkey, file_ext, blurb, and info will be searched when enter is pressed in the search field, include whitespace by enclosing search term in double quotes, allow specifying which field to search by using the idiom 'field=term' where field is any of the previous field names (or more user-centric aliases: database for dbkey, etc.), (GUI filters as an alternate means to accomplish field specifiers to be added soon); Allow showing and hiding search input; Tweak style on panel-header buttons; pack scripts Affected #: 14 files diff -r f166886d97a0e7dcb926c2e5f83db8f52982748f -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -664,6 +664,13 @@ this._renderTags( $newRender ); this._renderAnnotation( $newRender ); } + // button for opening search + faIconButton({ + title : _l( 'Search datasets' ), + classes : 'history-search-btn', + faIcon : 'fa-search' + }).prependTo( $newRender.find( '.history-secondary-actions' ) ); + this._setUpBehaviours( $newRender ); // render hda views (if any and any shown (show_deleted/hidden) @@ -696,10 +703,9 @@ }); }, - /** Set up HistoryPanel js/widget behaviours - */ - //TODO: these should be either sub-MVs, or handled by events + /** Set up HistoryPanel js/widget behaviours */ _setUpBehaviours : function( $where ){ + //TODO: these should be either sub-MVs, or handled by events $where = $where || this.$el; $where.find( '[title]' ).tooltip({ placement: 'bottom' }); @@ -757,7 +763,8 @@ events : { // allow (error) messages to be clicked away //TODO: switch to common close (X) idiom - 'click .message-container' : 'clearMessages' + 'click .message-container' : 'clearMessages', + 'click .history-search-btn' : 'toggleSearchControls' }, /** Update the history size display (curr. upper right of panel). @@ -843,7 +850,11 @@ $searchInput = this.renderSearchControls().hide(); this.$el.find( '.history-title' ).before( $searchInput ); } - $searchInput.slideToggle( this.fxSpeed ); + $searchInput.slideToggle( this.fxSpeed, function(){ + if( $( this ).is( ':visible' ) ){ + $( this ).find( 'input' ).focus(); + } + }); }, // ........................................................................ multi-select of hdas diff -r f166886d97a0e7dcb926c2e5f83db8f52982748f -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -590,7 +590,7 @@ // a button for clearing the search bar, placed on the right hand side function clearBtnTemplate(){ - return '<span class="search-clear fa fa-times-circle"></span>'; + return '<span class="search-clear fa fa-times-circle" title="' + _l( 'clear search (esc)' ) + '"></span>'; } function $clearBtn(){ //TODO: to base.less @@ -602,6 +602,7 @@ 'line-height': '23px', color : 'grey' }) + .tooltip({ placement: 'bottom' }) .click( function( event ){ clearSearchInput.call( this, event ); }); diff -r f166886d97a0e7dcb926c2e5f83db8f52982748f -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 static/scripts/packed/galaxy.masthead.js --- a/static/scripts/packed/galaxy.masthead.js +++ b/static/scripts/packed/galaxy.masthead.js @@ -1,1 +1,1 @@ -define(["utils/galaxy.utils"],function(c){var a=Backbone.View.extend({el_masthead:"#everything",options:null,list:{},itemLast:null,itemCounter:0,$background:null,backgroundVisible:false,initialize:function(f){this.options=f;$("body").off();this.setElement($(this._template(f)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var e=this;window.onbeforeunload=function(){var h="";for(key in e.list){if(e.list[key].options.on_unload){var g=e.list[key].options.on_unload();if(g){h+=g+" "}}}if(h!=""){return h}}},events:{click:"_eventRefresh",mousedown:function(f){f.preventDefault()}},append:function(e){return this._add(e,true)},prepend:function(e){return this._add(e,false)},_add:function(g,f){var e=$(this.el).find("#"+g.mastheadLocation);if(e){var h="masthead-item-"+this.itemCounter++;var i=$(g.el);i.attr("id",h);i.addClass("masthead-item");if(f){e.append(i)}else{e.prepend(i)}this.list[h]=g;return h}return null},_eventRefresh:function(h){var i=$(h.target).closest(".masthead-item");if(i.length){i=i.attr("id")}if(this.itemLast&&this.itemLast!=i){var g=this.list[this.itemLast];if(g){if(g.mastheadReset){g.mastheadReset()}}}var f=false;if(i){var g=this.list[i];if(g){if(g.mastheadReset){if(this.itemLast==i){f=this.backgroundVisible?false:true}else{f=true}}}}if(f){this.$background.show()}else{this.$background.hide()}this.backgroundVisible=f;this.itemLast=i},_templateItem:function(e){return'<div id="'+e+'" class="masthead-item"></div>'},_template:function(e){return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+e.logo_url+'"><img border="0" src="'+galaxy_config.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+e.brand+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});var b=Backbone.View.extend({options:{id:"galaxy-icon",icon:"fa-cog",tooltip:"galaxy-icon",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},mastheadLocation:"iconbar",initialize:function(f){if(f){this.options=_.defaults(f,this.options)}this.setElement($(this._template(this.options)));var e=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",e.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(e){$(this.el).find(".icon").removeClass(this.options.icon).addClass(e);this.options.icon=e},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(e){$(this.el).find(".number").text(e)},_template:function(f){var e="<div id="+f.id+' class="symbol"><div class="icon fa fa-2x '+f.icon+'"></div>';if(f.with_number){e+='<div class="number"></div>'}e+="</div>";return e}});var d=Backbone.View.extend({options:{id:"",title:"Title",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true},mastheadLocation:"navbar",$menu:null,menuVisible:false,events:{"click .head":"_eventClickHead"},initialize:function(e){if(e){this.options=_.defaults(e,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},addMenu:function(g){var h={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(g){h=_.defaults(g,h)}if(h.content&&h.content.indexOf("//")===-1){h.content=galaxy_config.root+h.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".menu")}var f=$(this._templateMenuItem(h));this.$menu.append(f);var e=this;f.on("click",function(i){i.preventDefault();e._hideMenu();if(e.options.target==="_blank"){return true}Galaxy.frame.add(g)});if(h.divider){this.$menu.append($(this._templateDivider()))}},mastheadReset:function(){this._hideMenu()},_hideMenu:function(){if(this.$menu&&this.menuVisible){this.$menu.hide();this.menuVisible=false}},_eventClickHead:function(f){f.preventDefault();if(this.$menu){if(!this.menuVisible){this.$menu.show();this.menuVisible=true}else{this.$menu.hide();this.menuVisible=false}}else{Galaxy.frame.add(this.options)}},_templateMenuItem:function(e){return'<li><a href="'+e.content+'" target="'+e.target+'">'+e.title+"</a></li>"},_templateMenu:function(){return'<ul class="menu dropdown-menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(f){var e='<ul class="nav navbar-nav" border="0" cellspacing="0"><li class="root dropdown" style=""><a class="head dropdown-toggle" data-toggle="dropdown" target="'+f.target+'" href="'+f.content+'">'+f.title+'<b class="symbol"></b></a></li></ul>';return e}});return{GalaxyMasthead:a,GalaxyMastheadTab:d,GalaxyMastheadIcon:b}}); \ No newline at end of file +define(["utils/galaxy.utils"],function(c){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(f){this.options=f;$("body").off();this.setElement($(this._template(f)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var e=this;window.onbeforeunload=function(){var h="";for(key in e.list){if(e.list[key].options.on_unload){var g=e.list[key].options.on_unload();if(g){h+=g+" "}}}if(h!=""){return h}}},events:{click:"_click",mousedown:function(f){f.preventDefault()}},append:function(e){return this._add(e,true)},prepend:function(e){return this._add(e,false)},highlight:function(f){var e=$(this.el).find("#"+f+"> li");if(e){e.addClass("active")}},_add:function(h,f){var e=$(this.el).find("#"+h.location);if(e){var g=$(h.el);g.addClass("masthead-item");if(f){e.append(g)}else{e.prepend(g)}this.list.push(h)}return null},_click:function(h){var g=$(this.el).find(".popup");if(g){g.hide()}var f=$(h.target).closest(".masthead-item").find(".popup");if($(h.target).hasClass("head")){f.show();this.$background.show()}else{this.$background.hide()}},_template:function(e){return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+e.logo_url+'"><img border="0" src="'+galaxy_config.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+e.brand+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},location:"iconbar",initialize:function(f){if(f){this.options=_.defaults(f,this.options)}this.setElement($(this._template(this.options)));var e=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",e.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(e){$(this.el).find(".icon").removeClass(this.options.icon).addClass(e);this.options.icon=e},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(e){$(this.el).find(".number").text(e)},_template:function(f){var e='<div id="'+f.id+'" class="symbol"><div class="icon fa fa-2x '+f.icon+'"></div>';if(f.with_number){e+='<div class="number"></div>'}e+="</div>";return e}});var d=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(e){if(e){this.options=_.defaults(e,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(g){var h={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(g){h=_.defaults(g,h)}if(h.content&&h.content.indexOf("//")===-1){h.content=galaxy_config.root+h.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var f=$(this._templateMenuItem(h));this.$menu.append(f);var e=this;f.on("click",function(i){i.preventDefault();if(e.options.target==="_blank"){return true}Galaxy.frame.add(g)});if(h.divider){this.$menu.append($(this._templateDivider()))}},_head:function(f){f.preventDefault();if(!this.$menu){Galaxy.frame.add(this.options)}},_templateMenuItem:function(e){return'<li><a href="'+e.content+'" target="'+e.target+'">'+e.title+"</a></li>"},_templateMenu:function(){return'<ul class="popup dropdown-menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(f){var e='<ul id="'+f.id+'" class="nav navbar-nav" border="0" cellspacing="0"><li class="root dropdown" style=""><a class="head dropdown-toggle" data-toggle="dropdown" target="'+f.target+'" href="'+f.content+'">'+f.title+'<b class="symbol"></b></a></li></ul>';return e}});return{GalaxyMasthead:a,GalaxyMastheadTab:d,GalaxyMastheadIcon:b}}); \ No newline at end of file diff -r f166886d97a0e7dcb926c2e5f83db8f52982748f -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 static/scripts/packed/galaxy.menu.js --- a/static/scripts/packed/galaxy.menu.js +++ b/static/scripts/packed/galaxy.menu.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var d=new b.GalaxyMastheadTab({title:"Analyze Data",content:"root/index"});this.masthead.append(d);var c=new b.GalaxyMastheadTab({title:"Workflow",content:"workflow"});this.masthead.append(c);var g=new b.GalaxyMastheadTab({title:"Shared Data",content:"library/index"});g.addMenu({title:"Data Libraries",content:"library/index",divider:true});g.addMenu({title:"Published Histories",content:"history/list_published"});g.addMenu({title:"Published Workflows",content:"workflow/list_published"});g.addMenu({title:"Published Visualizations",content:"visualization/list_published"});g.addMenu({title:"Published Pages",content:"page/list_published"});this.masthead.append(g);if(this.options.user.requests){var h=new b.GalaxyMastheadTab({title:"Lab"});h.addMenu({title:"Sequencing Requests",content:"requests/index"});h.addMenu({title:"Find Samples",content:"requests/find_samples_index"});h.addMenu({title:"Help",content:this.options.lims_doc_url});this.masthead.append(h)}var k=new b.GalaxyMastheadTab({title:"Visualization",content:"visualization/list"});k.addMenu({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});k.addMenu({title:"Saved Visualizations",content:"visualization/list",target:"_frame"});this.masthead.append(k);if(this.options.enable_cloud_launch){var e=new b.GalaxyMastheadTab({title:"Cloud",content:"cloudlaunch/index"});e.addMenu({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(e)}if(this.options.is_admin_user){var f=new b.GalaxyMastheadTab({title:"Admin",content:"admin/index",extra_class:"admin-only"});this.masthead.append(f)}var j=new b.GalaxyMastheadTab({title:"Help"});if(this.options.biostar_url){j.addMenu({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});j.addMenu({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}j.addMenu({title:"Support",content:this.options.support_url,target:"_blank"});j.addMenu({title:"Search",content:this.options.search_url,target:"_blank"});j.addMenu({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});j.addMenu({title:"Videos",content:this.options.screencasts_url,target:"_blank"});j.addMenu({title:"Wiki",content:this.options.wiki_url,target:"_blank"});j.addMenu({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(!this.options.terms_url){j.addMenu({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(j);if(!this.options.user.valid){var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedout-only"});i.addMenu({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){i.addMenu({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(i)}else{var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedin-only"});i.addMenu({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){i.addMenu({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{i.addMenu({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});i.addMenu({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});i.addMenu({title:"Logout",content:"user/logout",target:"_top",divider:true})}i.addMenu({title:"Saved Histories",content:"history/list",target:"galaxy_main"});i.addMenu({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});i.addMenu({title:"Saved Pages",content:"page/list",target:"_top"});i.addMenu({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){i.addMenu({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(i)}}});return{GalaxyMenu:a}}); \ No newline at end of file +define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var d=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"root/index"});this.masthead.append(d);var c=new b.GalaxyMastheadTab({id:"workflow",title:"Workflow",content:"workflow"});this.masthead.append(c);var g=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index"});g.add({title:"Data Libraries",content:"library/index",divider:true});g.add({title:"Published Histories",content:"history/list_published"});g.add({title:"Published Workflows",content:"workflow/list_published"});g.add({title:"Published Visualizations",content:"visualization/list_published"});g.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(g);if(this.options.user.requests){var h=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});h.add({title:"Sequencing Requests",content:"requests/index"});h.add({title:"Find Samples",content:"requests/find_samples_index"});h.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(h)}var k=new b.GalaxyMastheadTab({id:"visualization",title:"Visualization",content:"visualization/list"});k.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});k.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"});this.masthead.append(k);if(this.options.enable_cloud_launch){var e=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});e.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(e)}if(this.options.is_admin_user){var f=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin/index",extra_class:"admin-only"});this.masthead.append(f)}var j=new b.GalaxyMastheadTab({id:"help",title:"Help"});if(this.options.biostar_url){j.add({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});j.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}j.add({title:"Support",content:this.options.support_url,target:"_blank"});j.add({title:"Search",content:this.options.search_url,target:"_blank"});j.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});j.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});j.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});j.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(!this.options.terms_url){j.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(j);if(!this.options.user.valid){var i=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only"});i.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){i.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(i)}else{var i=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only"});i.add({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){i.add({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{i.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});i.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});i.add({title:"Logout",content:"user/logout",target:"_top",divider:true})}i.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});i.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});i.add({title:"Saved Pages",content:"page/list",target:"_top"});i.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){i.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(i)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file diff -r f166886d97a0e7dcb926c2e5f83db8f52982748f -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(f,b,a){var c=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(g){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([g],[true])))},removeExpandedHda:function(g){this.save("expandedHdas",_.omit(this.get("expandedHdas"),g))},toString:function(){return"HistoryPanelPrefs("+this.id+")"}});c.historyStorageKey=function e(g){if(!g){throw new Error("HistoryPanelPrefs.historyStorageKey needs valid id: "+g)}return("history:"+g)};var d=Backbone.View.extend(LoggableMixin).extend({HDAView:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(g){g=g||{};if(g.logger){this.logger=g.logger}this.log(this+".initialize:",g);this._setUpListeners();this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.filters=[];if(this.model){this._setUpWebStorage(g.initiallyExpanded,g.show_deleted,g.show_hidden);this._setUpModelEventHandlers()}if(g.onready){g.onready.call(this)}},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(g){this.log(this+"",arguments)},this)}},errorHandler:function(i,l,h,k,j){var g=this._parseErrorMessage(i,l,h,k,j);if(l&&l.status===0&&l.readyState===0){}else{if(l&&l.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",g.message,g.details)})}else{this.displayMessage("error",g.message,g.details)}}}},_parseErrorMessage:function(j,n,i,m,l){var h=Galaxy.currUser,g={message:this._bePolite(m),details:{user:(h instanceof User)?(h.toJSON()):(h+""),source:(j instanceof Backbone.Model)?(j.toJSON()):(j+""),xhr:n,options:(n)?(_.omit(i,"xhr")):(i)}};_.extend(g.details,l||{});if(n&&_.isFunction(n.getAllResponseHeaders)){var k=n.getAllResponseHeaders();k=_.compact(k.split("\n"));k=_.map(k,function(o){return o.split(": ")});g.details.xhr.responseHeaders=_.object(k)}return g},_bePolite:function(g){g=g||_l("An error occurred while getting updates from the server");return g+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(h){var g=this;return this.loadHistoryWithHDADetails("current",h).then(function(j,i){g.trigger("current-history",g)})},switchToHistory:function(j,i){var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories/"+j+"/set_as_current")};return this.loadHistoryWithHDADetails(j,i,h).then(function(l,k){g.trigger("switched-history",g)})},createNewHistory:function(i){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,i,h).then(function(k,j){g.trigger("new-history",g)})},loadHistoryWithHDADetails:function(j,i,h,l){var g=this,k=function(m){return g.getExpandedHdaIds(m.id)};return this.loadHistory(j,i,h,l,k)},loadHistory:function(j,i,h,m,k){this.trigger("loading-history",this);i=i||{};var g=this;var l=f.History.getHistoryData(j,{historyFn:h,hdaFn:m,hdaDetailIds:i.initiallyExpanded||k});return this._loadHistoryFromXHR(l,i).fail(function(p,n,o){g.trigger("error",g,p,i,_l("An error was encountered while "+n),{historyId:j,history:o||{}})}).always(function(){g.trigger("loading-done",g)})},_loadHistoryFromXHR:function(i,h){var g=this;i.then(function(j,k){g.setModel(j,k,h)});i.fail(function(k,j){g.render()});return i},setModel:function(i,g,h){h=h||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){i.user=Galaxy.currUser.toJSON()}this.model=new f.History(i,g,h);this._setUpWebStorage(h.initiallyExpanded,h.show_deleted,h.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},refreshHdas:function(h,g){if(this.model){return this.model.refresh(h,g)}return $.when()},_setUpWebStorage:function(h,g,i){this.storage=new c({id:c.historyStorageKey(this.model.get("id"))});if(_.isObject(h)){this.storage.set("exandedHdas",h)}if(_.isBoolean(g)){this.storage.set("show_deleted",g)}if(_.isBoolean(i)){this.storage.set("show_hidden",i)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var g in sessionStorage){if(g.indexOf("history:")===0){sessionStorage.removeItem(g)}}},getStoredOptions:function(h){if(!h||h==="current"){return(this.storage)?(this.storage.get()):({})}var g=sessionStorage.getItem(c.historyStorageKey(h));return(g===null)?({}):(JSON.parse(g))},getExpandedHdaIds:function(g){var h=this.getStoredOptions(g).expandedHdas;return((_.isEmpty(h))?([]):(_.keys(h)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(h,j,g,i){this.errorHandler(h,j,g,i)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(g){this.model.fetch()},this);this.model.hdas.on("state:ready",function(h,i,g){if((!h.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[h.id])}},this)},addHdaView:function(j){this.log("add."+this,j);var h=this;if(!j.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function i(l){var k=h.$el.find(h.emptyMsgSelector);if(k.is(":visible")){k.fadeOut(h.fxSpeed,l)}else{l()}},function g(l){h.scrollToTop();var k=h.$el.find(h.datasetsSelector);h.createHdaView(j).$el.hide().prependTo(k).slideDown(h.fxSpeed)}])},createHdaView:function(i){var h=i.get("id"),g=this.storage.get("expandedHdas")[h],j=new this.HDAView({model:i,expanded:g,hasUser:this.model.hasUser(),logger:this.logger});this._setUpHdaListeners(j);this.hdaViews[h]=j;return j.render()},_setUpHdaListeners:function(h){var g=this;h.on("body-expanded",function(i){g.storage.addExpandedHda(i)});h.on("body-collapsed",function(i){g.storage.removeExpandedHda(i)});h.on("error",function(j,l,i,k){g.errorHandler(j,l,i,k)})},handleHdaDeletionChange:function(g){if(g.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[g.id])}},handleHdaVisibleChange:function(g){if(g.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[g.id])}},removeHdaView:function(h){if(!h){return}var g=this;h.$el.fadeOut(g.fxSpeed,function(){h.off();h.remove();delete g.hdaViews[h.model.id];if(_.isEmpty(g.hdaViews)){g.$el.find(g.emptyMsgSelector).fadeIn(g.fxSpeed,function(){g.trigger("empty-history",g)})}})},render:function(i,j){i=(i===undefined)?(this.fxSpeed):(i);var g=this,h;if(this.model){h=this.renderModel()}else{h=this.renderWithoutModel()}$(g).queue("fx",[function(k){if(i&&g.$el.is(":visible")){g.$el.fadeOut(i,k)}else{k()}},function(k){g.$el.empty();if(h){g.$el.append(h.children())}k()},function(k){if(i&&!g.$el.is(":visible")){g.$el.fadeIn(i,k)}else{k()}},function(k){if(j){j.call(this)}g.trigger("rendered",this);k()}]);return this},renderWithoutModel:function(){var g=$("<div/>"),h=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return g.append(h)},renderModel:function(){var g=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){g.append(d.templates.anonHistoryPanel(this.model.toJSON()))}else{g.append(d.templates.historyPanel(this.model.toJSON()));this._renderTags(g);this._renderAnnotation(g)}this._setUpBehaviours(g);this.renderHdas(g);return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".history-secondary-actions"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".history-secondary-actions"))})},_setUpBehaviours:function(g){g=g||this.$el;g.find("[title]").tooltip({placement:"bottom"});if(!this.model||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){return}var h=this;g.find(".history-name").make_text_editable({on_finish:function(i){g.find(".history-name").text(i);h.model.save({name:i}).fail(function(){g.find(".history-name").text(h.model.previous("name"))})}})},renderHdas:function(i){i=i||this.$el;this.hdaViews={};var h=this,g=i.find(this.datasetsSelector),j=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);g.empty();if(j.length){j.each(function(k){g.prepend(h.createHdaView(k).$el)});i.find(this.emptyMsgSelector).hide()}else{i.find(this.emptyMsgSelector).show()}return this.hdaViews},events:{"click .message-container":"clearMessages"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(g){g.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},renderSearchControls:function(){var g=this;g.model.hdas.fetchAllDetails({silent:true});function i(j){g.searchFor=j;g.filters=[function(k){return k.matchesAll(g.searchFor)}];g.trigger("search:searching",j,g);g.renderHdas()}function h(){g.searchFor="";g.filters=[];g.trigger("search:clear",g);g.renderHdas()}return searchInput({initialVal:g.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onsearch:i,onclear:h}).addClass("history-search-controls").css("padding","0px 0px 8px 0px")},toggleSearchControls:function(){var g=this.$el.find(".history-search-controls");if(!g.size()){g=this.renderSearchControls().hide();this.$el.find(".history-title").before(g)}g.slideToggle(this.fxSpeed)},showSelect:function(g){_.each(this.hdaViews,function(h){h.showSelect(g)})},hideSelect:function(g){_.each(this.hdaViews,function(h){h.hideSelect(g)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(g){return g.selected})},showLoadingIndicator:function(h,g,i){g=(g!==undefined)?(g):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,i)}else{this.$el.fadeOut(g);this.indicator.show(h,g,i)}},hideLoadingIndicator:function(g,h){g=(g!==undefined)?(g):(this.fxSpeed);if(this.indicator){this.indicator.hide(g,h)}},displayMessage:function(l,m,k){var i=this;this.scrollToTop();var j=this.$el.find(this.msgsSelector),g=$("<div/>").addClass(l+"message").html(m);if(!_.isEmpty(k)){var h=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(i.messageToModalOptions(l,m,k));return false});g.append(" ",h)}return j.html(g)},messageToModalOptions:function(k,m,j){var g=this,l=$("<div/>"),i={title:"Details"};function h(n){n=_.omit(n,_.functions(n));return["<table>",_.map(n,function(p,o){p=(_.isObject(p))?(h(p)):(p);return'<tr><td style="vertical-align: top; color: grey">'+o+'</td><td style="padding-left: 8px">'+p+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(j)){i.body=l.append(h(j))}else{i.body=l.html(j)}i.buttons={Ok:function(){Galaxy.modal.hide();g.clearMessages()}};return i},clearMessages:function(){var g=this.$el.find(this.msgsSelector);g.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(g){this.$el.parent().scrollTop(g)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(h,i){if(!i){this.$el.parent().parent().scrollTop(h);return this}var g=window,j=this.$el.parent().parent(),l=$(g).innerHeight(),k=(l/2)-(i/2);$(j).scrollTop(h-k);return this},scrollToId:function(h){if((!h)||(!this.hdaViews[h])){return this}var g=this.hdaViews[h].$el;this.scrollIntoView(g.offset().top,g.outerHeight());return this},scrollToHid:function(g){var h=this.model.hdas.getByHid(g);if(!h){return this}return this.scrollToId(h.id)},connectToQuotaMeter:function(g){if(!g){return this}this.listenTo(g,"quota:over",this.showQuotaMessage);this.listenTo(g,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(g&&g.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var g=this.$el.find(".quota-message");if(g.is(":hidden")){g.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var g=this.$el.find(".quota-message");if(!g.is(":hidden")){g.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(g){if(!g){return this}this.on("new-storage",function(i,h){if(g&&i){g.findItemByHtml(_l("Include Deleted Datasets")).checked=i.get("show_deleted");g.findItemByHtml(_l("Include Hidden Datasets")).checked=i.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:d}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(f,b,a){var c=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(g){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([g],[true])))},removeExpandedHda:function(g){this.save("expandedHdas",_.omit(this.get("expandedHdas"),g))},toString:function(){return"HistoryPanelPrefs("+this.id+")"}});c.historyStorageKey=function e(g){if(!g){throw new Error("HistoryPanelPrefs.historyStorageKey needs valid id: "+g)}return("history:"+g)};var d=Backbone.View.extend(LoggableMixin).extend({HDAView:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(g){g=g||{};if(g.logger){this.logger=g.logger}this.log(this+".initialize:",g);this._setUpListeners();this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.filters=[];if(this.model){this._setUpWebStorage(g.initiallyExpanded,g.show_deleted,g.show_hidden);this._setUpModelEventHandlers()}if(g.onready){g.onready.call(this)}},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(g){this.log(this+"",arguments)},this)}},errorHandler:function(i,l,h,k,j){var g=this._parseErrorMessage(i,l,h,k,j);if(l&&l.status===0&&l.readyState===0){}else{if(l&&l.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",g.message,g.details)})}else{this.displayMessage("error",g.message,g.details)}}}},_parseErrorMessage:function(j,n,i,m,l){var h=Galaxy.currUser,g={message:this._bePolite(m),details:{user:(h instanceof User)?(h.toJSON()):(h+""),source:(j instanceof Backbone.Model)?(j.toJSON()):(j+""),xhr:n,options:(n)?(_.omit(i,"xhr")):(i)}};_.extend(g.details,l||{});if(n&&_.isFunction(n.getAllResponseHeaders)){var k=n.getAllResponseHeaders();k=_.compact(k.split("\n"));k=_.map(k,function(o){return o.split(": ")});g.details.xhr.responseHeaders=_.object(k)}return g},_bePolite:function(g){g=g||_l("An error occurred while getting updates from the server");return g+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(h){var g=this;return this.loadHistoryWithHDADetails("current",h).then(function(j,i){g.trigger("current-history",g)})},switchToHistory:function(j,i){var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories/"+j+"/set_as_current")};return this.loadHistoryWithHDADetails(j,i,h).then(function(l,k){g.trigger("switched-history",g)})},createNewHistory:function(i){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,i,h).then(function(k,j){g.trigger("new-history",g)})},loadHistoryWithHDADetails:function(j,i,h,l){var g=this,k=function(m){return g.getExpandedHdaIds(m.id)};return this.loadHistory(j,i,h,l,k)},loadHistory:function(j,i,h,m,k){this.trigger("loading-history",this);i=i||{};var g=this;var l=f.History.getHistoryData(j,{historyFn:h,hdaFn:m,hdaDetailIds:i.initiallyExpanded||k});return this._loadHistoryFromXHR(l,i).fail(function(p,n,o){g.trigger("error",g,p,i,_l("An error was encountered while "+n),{historyId:j,history:o||{}})}).always(function(){g.trigger("loading-done",g)})},_loadHistoryFromXHR:function(i,h){var g=this;i.then(function(j,k){g.setModel(j,k,h)});i.fail(function(k,j){g.render()});return i},setModel:function(i,g,h){h=h||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){i.user=Galaxy.currUser.toJSON()}this.model=new f.History(i,g,h);this._setUpWebStorage(h.initiallyExpanded,h.show_deleted,h.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},refreshHdas:function(h,g){if(this.model){return this.model.refresh(h,g)}return $.when()},_setUpWebStorage:function(h,g,i){this.storage=new c({id:c.historyStorageKey(this.model.get("id"))});if(_.isObject(h)){this.storage.set("exandedHdas",h)}if(_.isBoolean(g)){this.storage.set("show_deleted",g)}if(_.isBoolean(i)){this.storage.set("show_hidden",i)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var g in sessionStorage){if(g.indexOf("history:")===0){sessionStorage.removeItem(g)}}},getStoredOptions:function(h){if(!h||h==="current"){return(this.storage)?(this.storage.get()):({})}var g=sessionStorage.getItem(c.historyStorageKey(h));return(g===null)?({}):(JSON.parse(g))},getExpandedHdaIds:function(g){var h=this.getStoredOptions(g).expandedHdas;return((_.isEmpty(h))?([]):(_.keys(h)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(h,j,g,i){this.errorHandler(h,j,g,i)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(g){this.model.fetch()},this);this.model.hdas.on("state:ready",function(h,i,g){if((!h.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[h.id])}},this)},addHdaView:function(j){this.log("add."+this,j);var h=this;if(!j.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function i(l){var k=h.$el.find(h.emptyMsgSelector);if(k.is(":visible")){k.fadeOut(h.fxSpeed,l)}else{l()}},function g(l){h.scrollToTop();var k=h.$el.find(h.datasetsSelector);h.createHdaView(j).$el.hide().prependTo(k).slideDown(h.fxSpeed)}])},createHdaView:function(i){var h=i.get("id"),g=this.storage.get("expandedHdas")[h],j=new this.HDAView({model:i,expanded:g,hasUser:this.model.hasUser(),logger:this.logger});this._setUpHdaListeners(j);this.hdaViews[h]=j;return j.render()},_setUpHdaListeners:function(h){var g=this;h.on("body-expanded",function(i){g.storage.addExpandedHda(i)});h.on("body-collapsed",function(i){g.storage.removeExpandedHda(i)});h.on("error",function(j,l,i,k){g.errorHandler(j,l,i,k)})},handleHdaDeletionChange:function(g){if(g.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[g.id])}},handleHdaVisibleChange:function(g){if(g.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[g.id])}},removeHdaView:function(h){if(!h){return}var g=this;h.$el.fadeOut(g.fxSpeed,function(){h.off();h.remove();delete g.hdaViews[h.model.id];if(_.isEmpty(g.hdaViews)){g.$el.find(g.emptyMsgSelector).fadeIn(g.fxSpeed,function(){g.trigger("empty-history",g)})}})},render:function(i,j){i=(i===undefined)?(this.fxSpeed):(i);var g=this,h;if(this.model){h=this.renderModel()}else{h=this.renderWithoutModel()}$(g).queue("fx",[function(k){if(i&&g.$el.is(":visible")){g.$el.fadeOut(i,k)}else{k()}},function(k){g.$el.empty();if(h){g.$el.append(h.children())}k()},function(k){if(i&&!g.$el.is(":visible")){g.$el.fadeIn(i,k)}else{k()}},function(k){if(j){j.call(this)}g.trigger("rendered",this);k()}]);return this},renderWithoutModel:function(){var g=$("<div/>"),h=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return g.append(h)},renderModel:function(){var g=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){g.append(d.templates.anonHistoryPanel(this.model.toJSON()))}else{g.append(d.templates.historyPanel(this.model.toJSON()));this._renderTags(g);this._renderAnnotation(g)}faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"}).prependTo(g.find(".history-secondary-actions"));this._setUpBehaviours(g);this.renderHdas(g);return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".history-secondary-actions"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".history-secondary-actions"))})},_setUpBehaviours:function(g){g=g||this.$el;g.find("[title]").tooltip({placement:"bottom"});if(!this.model||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){return}var h=this;g.find(".history-name").make_text_editable({on_finish:function(i){g.find(".history-name").text(i);h.model.save({name:i}).fail(function(){g.find(".history-name").text(h.model.previous("name"))})}})},renderHdas:function(i){i=i||this.$el;this.hdaViews={};var h=this,g=i.find(this.datasetsSelector),j=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);g.empty();if(j.length){j.each(function(k){g.prepend(h.createHdaView(k).$el)});i.find(this.emptyMsgSelector).hide()}else{i.find(this.emptyMsgSelector).show()}return this.hdaViews},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(g){g.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},renderSearchControls:function(){var g=this;g.model.hdas.fetchAllDetails({silent:true});function i(j){g.searchFor=j;g.filters=[function(k){return k.matchesAll(g.searchFor)}];g.trigger("search:searching",j,g);g.renderHdas()}function h(){g.searchFor="";g.filters=[];g.trigger("search:clear",g);g.renderHdas()}return searchInput({initialVal:g.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onsearch:i,onclear:h}).addClass("history-search-controls").css("padding","0px 0px 8px 0px")},toggleSearchControls:function(){var g=this.$el.find(".history-search-controls");if(!g.size()){g=this.renderSearchControls().hide();this.$el.find(".history-title").before(g)}g.slideToggle(this.fxSpeed,function(){if($(this).is(":visible")){$(this).find("input").focus()}})},showSelect:function(g){_.each(this.hdaViews,function(h){h.showSelect(g)})},hideSelect:function(g){_.each(this.hdaViews,function(h){h.hideSelect(g)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(g){return g.selected})},showLoadingIndicator:function(h,g,i){g=(g!==undefined)?(g):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,i)}else{this.$el.fadeOut(g);this.indicator.show(h,g,i)}},hideLoadingIndicator:function(g,h){g=(g!==undefined)?(g):(this.fxSpeed);if(this.indicator){this.indicator.hide(g,h)}},displayMessage:function(l,m,k){var i=this;this.scrollToTop();var j=this.$el.find(this.msgsSelector),g=$("<div/>").addClass(l+"message").html(m);if(!_.isEmpty(k)){var h=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(i.messageToModalOptions(l,m,k));return false});g.append(" ",h)}return j.html(g)},messageToModalOptions:function(k,m,j){var g=this,l=$("<div/>"),i={title:"Details"};function h(n){n=_.omit(n,_.functions(n));return["<table>",_.map(n,function(p,o){p=(_.isObject(p))?(h(p)):(p);return'<tr><td style="vertical-align: top; color: grey">'+o+'</td><td style="padding-left: 8px">'+p+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(j)){i.body=l.append(h(j))}else{i.body=l.html(j)}i.buttons={Ok:function(){Galaxy.modal.hide();g.clearMessages()}};return i},clearMessages:function(){var g=this.$el.find(this.msgsSelector);g.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(g){this.$el.parent().scrollTop(g)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(h,i){if(!i){this.$el.parent().parent().scrollTop(h);return this}var g=window,j=this.$el.parent().parent(),l=$(g).innerHeight(),k=(l/2)-(i/2);$(j).scrollTop(h-k);return this},scrollToId:function(h){if((!h)||(!this.hdaViews[h])){return this}var g=this.hdaViews[h].$el;this.scrollIntoView(g.offset().top,g.outerHeight());return this},scrollToHid:function(g){var h=this.model.hdas.getByHid(g);if(!h){return this}return this.scrollToId(h.id)},connectToQuotaMeter:function(g){if(!g){return this}this.listenTo(g,"quota:over",this.showQuotaMessage);this.listenTo(g,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(g&&g.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var g=this.$el.find(".quota-message");if(g.is(":hidden")){g.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var g=this.$el.find(".quota-message");if(!g.is(":hidden")){g.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(g){if(!g){return this}this.on("new-storage",function(i,h){if(g&&i){g.findItemByHtml(_l("Include Deleted Datasets")).checked=i.get("show_deleted");g.findItemByHtml(_l("Include Hidden Datasets")).checked=i.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:d}}); \ No newline at end of file diff -r f166886d97a0e7dcb926c2e5f83db8f52982748f -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var c=d.href||"javascript:void(0);",e=(d.target)?(' target="'+d.target+'"'):(""),b=(d.checked)?('<span class="fa fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var c=this;function a(e){$(document).off("click.close_popup");if(window.parent!==window){try{$(window.parent.document).off("click.close_popup")}catch(d){}}else{try{$("iframe#galaxy_main").contents().off("click.close_popup")}catch(d){}}c.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){try{$(window.parent.document).find("html").one("click.close_popup",a)}catch(b){}}else{try{$("iframe#galaxy_main").contents().one("click.close_popup",a)}catch(b){}}},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(d.attr("href")){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};var faIconButton=function(a){a=a||{};a.tooltipConfig=a.tooltipConfig||{placement:"bottom"};a.classes=["icon-btn"].concat(a.classes||[]);if(a.disabled){a.classes.push("disabled")}var b=['<a class="',a.classes.join(" "),'"',((a.title)?(' title="'+a.title+'"'):("")),((a.target)?(' target="'+a.target+'"'):("")),' href="',((a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};var searchInput=function(k){var a=27,h=13,i=$("<div/>"),b={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onsearch:function(l){},minSearchLen:0,escWillClear:true,oninit:function(){}};if(jQuery.type(k)==="object"){k=jQuery.extend(true,b,k)}function d(l){var m=$(this).parent().children("input");m.val("");m.trigger("clear:searchInput");k.onclear()}function j(m,l){$(this).trigger("search:searchInput",l);k.onsearch(l)}function c(){return['<input type="text" name="',k.name,'" placeholder="',k.placeholder,'" ','class="search-query ',k.classes,'" ',"/>"].join("")}function g(){return $(c()).css({width:"100%","padding-right":"24px"}).focus(function(l){$(this).select()}).keyup(function(m){if(m.which===a&&k.escWillClear){d.call(this,m)}else{var l=$(this).val();if((m.which===h)||(k.minSearchLen&&l.length>=k.minSearchLen)){j.call(this,m,l)}else{if(!l.length){d.call(this,m)}}}}).val(k.initialVal)}function f(){return'<span class="search-clear fa fa-times-circle"></span>'}function e(){return $(f()).css({position:"absolute",right:"15px","font-size":"1.4em","line-height":"23px",color:"grey"}).click(function(l){d.call(this,l)})}return i.append([g(),e()])};function LoadingIndicator(a,c){var b=this;c=jQuery.extend({cover:false},c||{});function d(){var e=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n");var g=$(e).hide().css(c.css||{position:"fixed"}),f=g.children(".loading-indicator-text");if(c.cover){g.css({"z-index":2,top:a.css("top"),bottom:a.css("bottom"),left:a.css("left"),right:a.css("right"),opacity:0.5,"background-color":"white","text-align":"center"});f=g.children(".loading-indicator-text").css({"margin-top":"20px"})}else{f=g.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"});f.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})}return g}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}; \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var c=d.href||"javascript:void(0);",e=(d.target)?(' target="'+d.target+'"'):(""),b=(d.checked)?('<span class="fa fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var c=this;function a(e){$(document).off("click.close_popup");if(window.parent!==window){try{$(window.parent.document).off("click.close_popup")}catch(d){}}else{try{$("iframe#galaxy_main").contents().off("click.close_popup")}catch(d){}}c.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){try{$(window.parent.document).find("html").one("click.close_popup",a)}catch(b){}}else{try{$("iframe#galaxy_main").contents().one("click.close_popup",a)}catch(b){}}},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var 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Click 'Get Data' on the left pane to start"}r+='<div class="history-controls">\n\n <div class="history-title">\n ';i=q["if"].call(s,s.name,{hash:{},inverse:p.noop,fn:p.program(1,o,w),data:w});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=q["if"].call(s,s.nice_size,{hash:{},inverse:p.noop,fn:p.program(4,m,w),data:w});if(i||i===0){r+=i}r+='\n\n <div class="history-secondary-actions">\n </div>\n </div>\n\n ';i=q["if"].call(s,s.deleted,{hash:{},inverse:p.noop,fn:p.program(6,k,w),data:w});if(i||i===0){r+=i}r+='\n\n <div class="message-container">\n ';i=q["if"].call(s,s.message,{hash:{},inverse:p.noop,fn:p.program(9,g,w),data:w});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:p.noop,fn:p.program(11,v,w),data:w};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+=".\n ";f={hash:{},inverse:p.noop,fn:p.program(13,u,w),data:w};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='.\n </div>\n \n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:p.noop,fn:p.program(15,t,w),data:w};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+="\n </div>";return r})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(h,s,q,l,w){this.compilerInfo=[4,">= 1.0.0"];q=this.merge(q,h.helpers);w=w||{};var r="",i,f,p=this,e="function",c=q.blockHelperMissing,d=this.escapeExpression;function o(B,A){var x="",z,y;x+='\n <div class="history-name" title="';y={hash:{},inverse:p.noop,fn:p.program(2,n,A),data:A};if(z=q.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!q.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+='">\n ';if(z=q.name){z=z.call(B,{hash:{},data:A})}else{z=B.name;z=typeof z===e?z.apply(B):z}x+=d(z)+"\n </div>\n ";return x}function n(y,x){return"Click to rename history"}function m(A,z){var x="",y;x+='\n <div class="history-size">';if(y=q.nice_size){y=y.call(A,{hash:{},data:z})}else{y=A.nice_size;y=typeof y===e?y.apply(A):y}x+=d(y)+"</div>\n ";return x}function k(B,A){var x="",z,y;x+='\n <div class="warningmessagesmall"><strong>\n ';y={hash:{},inverse:p.noop,fn:p.program(7,j,A),data:A};if(z=q.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!q.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </strong></div>\n ";return x}function j(y,x){return"You are currently viewing a deleted history!"}function g(A,z){var x="",y;x+='\n \n <div class="';if(y=q.status){y=y.call(A,{hash:{},data:z})}else{y=A.status;y=typeof y===e?y.apply(A):y}x+=d(y)+'message">';if(y=q.message){y=y.call(A,{hash:{},data:z})}else{y=A.message;y=typeof y===e?y.apply(A):y}x+=d(y)+"</div>\n ";return x}function v(y,x){return"You are over your disk quota"}function u(y,x){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function t(y,x){return"Your history is empty. 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false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){R.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:ad.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=(ae.type==="color"&&!ae.default_value?l.get_random_color():ae.default_value)});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input />").attr("id",am).attr("name",am).val(ax).css("float","left").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.prefs.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.prefs.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.content_div.text(o);if(ag.message){ad.content_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ad.content_div.append($("<span/>").text(" "));ad.content_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ad,af,ae){af=".group";n[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=n[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=n[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}n[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);n[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));n[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(A.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.prefs.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){A.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});A.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new j({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+x+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+x+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=R.Tool.extend({defaults:{track:null},initialize:function(ac){R.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var v=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new y.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new P(view,view,{name:ad.prefs.name});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(z+ag.message)}else{af(ag)}}})}});var E=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};E.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var j=Backbone.Model.extend({initialize:function(ad){var ac={};ab.each(ad.params,function(ae){ac[ae.key]=(ae.type==="color"&&!ae.default_value?l.get_random_color():ae.default_value)});if(ad.saved_values){ab.each(this.get("params"),function(ae){if(ae.key in ad.saved_values){ac[ae.key]=ad.saved_values[ae.key]}})}this.set("values",ac)},set_param_default_value:function(ad,ac){var ae=ab.find(this.get("params"),function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.get("params"),function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.get("values")[ac]!==ad){this.get("values")[ac]=ad;this.trigger("change:values");return true}else{return false}}});var a=Backbone.View.extend({render:function(){var aj=this.model;var ac=$("<div/>").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at<ao.length;at++){ai=ao[at];if(ai.hidden){continue}var am="param_"+at;var ax=aj.get("values")[ai.key];var az=$("<div class='form-row' />").appendTo(ak);az.append($("<label />").attr("for",am).text(ai.label+":"));if(ai.type==="bool"){az.append($('<input type="checkbox" />').attr("id",am).attr("name",am).attr("checked",ax))}else{if(ai.type==="text"){az.append($('<input type="text"/>').attr("id",am).val(ax).click(function(){$(this).select()}))}else{if(ai.type==="select"){var av=$("<select />").attr("id",am);for(var aq=0;aq<ai.options.length;aq++){$("<option/>").text(ai.options[aq].label).attr("value",ai.options[aq].value).appendTo(av)}av.val(ax);az.append(av)}else{if(ai.type==="color"){var ay=$("<div/>").appendTo(az),au=$("<input/>").attr({id:am,name:am}).val(ax).addClass("color-input").appendTo(ay).click(function(aB){$(".tooltip").removeClass("in");var aA=$(this).siblings(".tooltip").addClass("in");aA.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(aA).height()/2)+($(this).height()/2)}).show();aA.click(function(aC){aC.stopPropagation()});$(document).bind("click.color-picker",function(){aA.hide();$(document).unbind("click.color-picker")});aB.stopPropagation()}),ar=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("<div class='tooltip right' style='position: absolute;' />").appendTo(ay).hide(),an=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(aw),al=$("<div class='tooltip-arrow'></div>").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("<div/>").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("<input />").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("<div class='help'/>").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.prefs.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.prefs.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof D){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(o);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)<ag){ak=Math.floor(ac*S*af);am=new y.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(S*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new P(this.view,this.container,{name:this.prefs.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var D=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(D.prototype,r.prototype,N.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:r.prototype.can_draw,draw_helper:function(ad,ae,ac){if(ae>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new c(this,ah,al,ac,ad)}});var h=function(ad,ac,ae){this.mode="Histogram";N.call(this,ad,ac,ae)};q(h.prototype,r.prototype,N.prototype,{display_modes:C,config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var t=function(ad,ac,ae){this.mode="Heatmap";N.call(this,ad,ac,ae)};q(t.prototype,r.prototype,N.prototype,{display_modes:["Heatmap"],config_params:ab.union(r.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new c(this,ag,ai,af,ac.data)}});var d=function(ad,ac,ae){N.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(d.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get("values").connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof O){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,B,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar<au;ar++){var ah=am.data[ar];var at=false;var al;for(var aw=0,aB=ak.length;aw<aB;aw++){al=ak[aw];al.update_attrs(ah);if(!al.keep(ah)){at=true;break}}if(!at){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aA=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null),ay=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null),az=new (this.painter)(ai,ax,ac,this.prefs,ao,aA,ay,ae,function(aC){return ap.view.get_base_color(aC)});var av=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){av=az.draw(aq,ad.width,ad.height,aj,an);av.translation=-ag}return new O(ap,af,aj,ad,am.data,ao,am.message,all_slotted,av)}});var Z=function(ad,ac,ae){N.call(this,ad,ac,ae);this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,N.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(r.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new c(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.prefs,ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){N.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof M)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.prefs.show_labels&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file diff -r f166886d97a0e7dcb926c2e5f83db8f52982748f -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 static/scripts/templates/compiled/history-templates.js --- a/static/scripts/templates/compiled/history-templates.js +++ b/static/scripts/templates/compiled/history-templates.js @@ -507,7 +507,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions\">\n </div>\n </div>\n\n "; + buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n <div class=\"message-container\">\n "; diff -r f166886d97a0e7dcb926c2e5f83db8f52982748f -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -96,7 +96,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions\">\n </div>\n </div>\n\n "; + buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n <div class=\"message-container\">\n "; diff -r f166886d97a0e7dcb926c2e5f83db8f52982748f -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -16,8 +16,7 @@ <div class="history-size">{{nice_size}}</div> {{/if}} - <div class="history-secondary-actions"> - </div> + <div class="history-secondary-actions"></div></div> {{#if deleted}} diff -r f166886d97a0e7dcb926c2e5f83db8f52982748f -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1507,9 +1507,10 @@ .icon-button.link{background:url(../images/silk/link.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px} .icon-button.link-broken{background:url(../images/silk/link_break.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px} .workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px} -.icon-btn{display:inline-block;height:20px;width:20px;text-align:center;line-height:17px;border-radius:3px;border:1px solid rgba(0,0,0,0.1);background-color:rgba(0,0,0,0.05);color:#555;font-size:1.2em;cursor:pointer} +.icon-btn{display:inline-block;height:20px;width:20px;text-align:center;line-height:17px;font-size:1.2em;border-radius:3px;border:1px solid rgba(0,0,0,0.1);background-color:rgba(0,0,0,0.05);color:#555;cursor:pointer} .icon-btn:hover{background-color:white;color:maroon} .icon-btn.disabled{background-color:transparent;color:rgba(0,0,0,0.05)} +#history-refresh-button,#history-options-button{display:inline-block;height:20px;width:20px;text-align:center;line-height:17px;font-size:1.2em;padding:0px} .history-panel [class$="messagesmall"]{margin:0px} .history-panel .editable-text{border:solid transparent 1px} .history-panel .editable-text:hover{cursor:pointer;border:1px dotted #999999} diff -r f166886d97a0e7dcb926c2e5f83db8f52982748f -r a6044ab1ffe717adc08eb6e43eb1febdc8a265f3 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -34,13 +34,14 @@ // center the icon text-align: center; line-height: @icon-btn-size - 3; + font-size: 1.2em; + // colors and borders border-radius: 3px; border: 1px solid @icon-btn-border; background-color: @icon-btn-bg; color : @icon-btn-color; - font-size: 1.2em; cursor: pointer; // tweaks @@ -59,6 +60,19 @@ color: @icon-btn-bg; } +// ---------------------------------------------------------------------------- panel header buttons +#history-refresh-button, +#history-options-button { + display : inline-block; + height : @icon-btn-size; + width : @icon-btn-size; + text-align : center; + line-height : @icon-btn-size - 3; + font-size : 1.2em; + + padding: 0px; +} + // ---------------------------------------------------------------------------- history .history-panel { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Another attempt to fix nosetests' handling of rods.py.
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f166886d97a0/ Changeset: f166886d97a0 User: jmchilton Date: 2013-12-03 19:59:35 Summary: Another attempt to fix nosetests' handling of rods.py. Further dirtying @dannon's code :(, sorry. Affected #: 1 file diff -r 1d75d75f9f82b9f9e7c19ef7d9d5df5e1565c962 -r f166886d97a0e7dcb926c2e5f83db8f52982748f lib/galaxy/objectstore/rods.py --- a/lib/galaxy/objectstore/rods.py +++ b/lib/galaxy/objectstore/rods.py @@ -18,6 +18,9 @@ try: import galaxy.eggs galaxy.eggs.require( 'PyRods' ) +except Exception: + pass +try: import irods except ImportError: irods = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Remove unused get_missing_tool_dependencies in install_and_test_tool_shed_repositories/base/test_db_util.py.
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d75d75f9f82/ Changeset: 1d75d75f9f82 User: jmchilton Date: 2013-12-03 18:54:56 Summary: Remove unused get_missing_tool_dependencies in install_and_test_tool_shed_repositories/base/test_db_util.py. Looks to have been replaced by method with same name in install_and_test_tool_shed_repositories/functional_tests.py and would throw a NameError on repository_id if ever used. Affected #: 1 file diff -r 34d18fc63a7c9232dc23184094fef3f022e12036 -r 1d75d75f9f82b9f9e7c19ef7d9d5df5e1565c962 test/install_and_test_tool_shed_repositories/base/test_db_util.py --- a/test/install_and_test_tool_shed_repositories/base/test_db_util.py +++ b/test/install_and_test_tool_shed_repositories/base/test_db_util.py @@ -30,11 +30,6 @@ model.ToolShedRepository.table.c.installed_changeset_revision == changeset_revision ) ) \ .one() -def get_missing_tool_dependencies( repository ): - return sa_session.query( model.ToolDependency ) \ - .filter( and_( model.ToolDependency.table.c.tool_shed_repository_id == repository_id, - model.ToolDependency.table.c.status != model.ToolDependency.installation_status.INSTALLED ) ) \ - .all() def get_private_role( user ): for role in user.all_roles(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5dbfdeb3295f/ Changeset: 5dbfdeb3295f User: jmchilton Date: 2013-12-02 22:15:16 Summary: Delay problems with fluent logger dependencies until fluent logger used. Affected #: 1 file diff -r ef33472f0aa296e55fd811357e09366f9cee5467 -r 5dbfdeb3295f23eea643f74c100d3549c6ddafb7 lib/galaxy/util/log/fluent_log.py --- a/lib/galaxy/util/log/fluent_log.py +++ b/lib/galaxy/util/log/fluent_log.py @@ -5,15 +5,23 @@ import time import threading -import galaxy.eggs -galaxy.eggs.require( "fluent-logger" ) -galaxy.eggs.require( "msgpack_python" ) +try: + import galaxy.eggs + galaxy.eggs.require( "fluent-logger" ) + galaxy.eggs.require( "msgpack_python" ) +except Exception: + pass -from fluent.sender import FluentSender +try: + from fluent.sender import FluentSender +except ImportError: + FluentSender = None class FluentTraceLogger( object ): def __init__( self, name, host='localhost', port=24224 ): + if FluentSender is None: + raise Exception("Attempted to use FluentTraceLogger with not Fluent dependency available.") self.lock = threading.Lock() self.thread_local = threading.local() self.name = name @@ -36,4 +44,4 @@ if hasattr( self.thread_local, 'context' ): kwargs.update( self.thread_local.context ) self.lock.release() - self.sender.emit_with_time( label, int(time.time()), kwargs ) \ No newline at end of file + self.sender.emit_with_time( label, int(time.time()), kwargs ) https://bitbucket.org/galaxy/galaxy-central/commits/34d18fc63a7c/ Changeset: 34d18fc63a7c User: jmchilton Date: 2013-12-03 17:39:21 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #270) Delay potential problems with fluent logger dependencies until fluent logger used. Affected #: 1 file diff -r 5667c340ef5de4254e1c591bf1e20c10a078b2c1 -r 34d18fc63a7c9232dc23184094fef3f022e12036 lib/galaxy/util/log/fluent_log.py --- a/lib/galaxy/util/log/fluent_log.py +++ b/lib/galaxy/util/log/fluent_log.py @@ -5,15 +5,23 @@ import time import threading -import galaxy.eggs -galaxy.eggs.require( "fluent-logger" ) -galaxy.eggs.require( "msgpack_python" ) +try: + import galaxy.eggs + galaxy.eggs.require( "fluent-logger" ) + galaxy.eggs.require( "msgpack_python" ) +except Exception: + pass -from fluent.sender import FluentSender +try: + from fluent.sender import FluentSender +except ImportError: + FluentSender = None class FluentTraceLogger( object ): def __init__( self, name, host='localhost', port=24224 ): + if FluentSender is None: + raise Exception("Attempted to use FluentTraceLogger with not Fluent dependency available.") self.lock = threading.Lock() self.thread_local = threading.local() self.name = name @@ -36,4 +44,4 @@ if hasattr( self.thread_local, 'context' ): kwargs.update( self.thread_local.context ) self.lock.release() - self.sender.emit_with_time( label, int(time.time()), kwargs ) \ No newline at end of file + self.sender.emit_with_time( label, int(time.time()), kwargs ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Code cleanup for rendering the tool test results container in the tool shed.
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5667c340ef5d/ Changeset: 5667c340ef5d User: greg Date: 2013-12-03 17:32:00 Summary: Code cleanup for rendering the tool test results container in the tool shed. Affected #: 1 file diff -r a540510a3091ad7cfe3c4680c8bb04a20679e44f -r 5667c340ef5de4254e1c591bf1e20c10a078b2c1 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1052,7 +1052,6 @@ """Return a folder hierarchy containing tool dependencies.""" # This container is displayed only in the tool shed. if tool_test_results_dicts: - test_results_dict_id = 0 folder_id += 1 tool_test_results_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) multiple_tool_test_results_dicts = len( tool_test_results_dicts ) > 1 @@ -1061,9 +1060,29 @@ test_runs_folder = Folder( id=folder_id, key='test_runs', label='Test runs', parent=tool_test_results_root_folder ) tool_test_results_root_folder.folders.append( test_runs_folder ) for index, tool_test_results_dict in enumerate( tool_test_results_dicts ): + if len( tool_test_results_dict ) < 2: + # Skip tool test results that have only a 'test_environment' entry since this implies that only the preparation + # script check_repositories_for_functional_tests.py has run for that entry. + continue + # We have a dictionary that looks something like this: + # {'missing_test_components': [], + # 'failed_tests': [], + # 'passed_tests': + # [{'tool_id': 'effectiveT3', + # 'test_id': 'test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/...)', + # 'tool_version': '0.0.12'}, + # {'tool_id': 'effectiveT3', + # 'test_id': 'test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/...)', + # 'tool_version': '0.0.12'}], + # 'test_environment': + # {'python_version': '2.7.4', 'tool_shed_mercurial_version': '2.2.3', 'system': 'Linux 3.8.0-30-generic', + # 'tool_shed_database_version': 21, 'architecture': 'x86_64', 'galaxy_revision': '11573:a62c54ddbe2a', + # 'galaxy_database_version': 117, 'time_tested': '2013-12-03 09:11:48', 'tool_shed_revision': '11556:228156daa575'}, + # 'installation_errors': + # {'current_repository': [], 'repository_dependencies': [], 'tool_dependencies': []}}, test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) if test_environment_dict is None: - # the test environment entry will exist only if the preparation script check_re;ositories_for_functional_tests.py + # The test environment entry will exist only if the preparation script check_repositories_for_functional_tests.py # was executed prior to the ~/install_and_test_repositories/functional_tests.py script. If that did not occur, # we'll display test result, but the test_environment entries will not be complete. test_environment_dict = {} @@ -1074,10 +1093,9 @@ test_runs_folder.folders.append( containing_folder ) else: containing_folder = tool_test_results_root_folder - test_results_dict_id += 1 folder_id += 1 - folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) - containing_folder.folders.append( folder ) + test_environment_folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) + containing_folder.folders.append( test_environment_folder ) architecture = test_environment_dict.get( 'architecture', '' ) galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' ) galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' ) @@ -1096,21 +1114,21 @@ tool_shed_database_version=tool_shed_database_version, tool_shed_mercurial_version=tool_shed_mercurial_version, tool_shed_revision=tool_shed_revision ) - folder.test_environments.append( test_environment ) + test_environment_folder.test_environments.append( test_environment ) not_tested_dict = tool_test_results_dict.get( 'not_tested', {} ) if not_tested_dict: folder_id += 1 - folder = Folder( id=folder_id, key='not_tested', label='Not tested', parent=containing_folder ) - containing_folder.folders.append( folder ) + not_tested_folder = Folder( id=folder_id, key='not_tested', label='Not tested', parent=containing_folder ) + containing_folder.folders.append( not_tested_folder ) not_tested_id = 0 not_tested = NotTested( id=not_tested_id, reason=not_tested_dict.get( 'reason', '' ) ) - folder.not_tested.append( not_tested ) + not_tested_folder.not_tested.append( not_tested ) passed_tests_dicts = tool_test_results_dict.get( 'passed_tests', [] ) if passed_tests_dicts: folder_id += 1 - folder = Folder( id=folder_id, key='passed_tests', label='Tests that passed successfully', parent=containing_folder ) - containing_folder.folders.append( folder ) + passed_tests_folder = Folder( id=folder_id, key='passed_tests', label='Tests that passed successfully', parent=containing_folder ) + containing_folder.folders.append( passed_tests_folder ) passed_test_id = 0 for passed_tests_dict in passed_tests_dicts: passed_test_id += 1 @@ -1118,12 +1136,12 @@ test_id=passed_tests_dict.get( 'test_id' '' ), tool_id=passed_tests_dict.get( 'tool_id', '' ), tool_version=passed_tests_dict.get( 'tool_version', '' ) ) - folder.passed_tests.append( passed_test ) + passed_tests_folder.passed_tests.append( passed_test ) failed_tests_dicts = tool_test_results_dict.get( 'failed_tests', [] ) if failed_tests_dicts: folder_id += 1 - folder = Folder( id=folder_id, key='failed_tests', label='Tests that failed', parent=containing_folder ) - containing_folder.folders.append( folder ) + failed_tests_folder = Folder( id=folder_id, key='failed_tests', label='Tests that failed', parent=containing_folder ) + containing_folder.folders.append( failed_tests_folder ) failed_test_id = 0 for failed_tests_dict in failed_tests_dicts: # TODO: Remove this when invalid test data is eliminated. @@ -1136,12 +1154,15 @@ tool_id=failed_tests_dict.get( 'tool_id', '' ), tool_version=failed_tests_dict.get( 'tool_version', '' ), traceback=failed_tests_dict.get( 'traceback', '' ) ) - folder.failed_tests.append( failed_test ) + failed_tests_folder.failed_tests.append( failed_test ) missing_test_components_dicts = tool_test_results_dict.get( 'missing_test_components', [] ) if missing_test_components_dicts: folder_id += 1 - folder = Folder( id=folder_id, key='missing_test_components', label='Tools missing tests or test data', parent=containing_folder ) - containing_folder.folders.append( folder ) + missing_test_components_folder = Folder( id=folder_id, + key='missing_test_components', + label='Tools missing tests or test data', + parent=containing_folder ) + containing_folder.folders.append( missing_test_components_folder ) missing_test_component_id = 0 for missing_test_components_dict in missing_test_components_dicts: missing_test_component_id += 1 @@ -1150,7 +1171,7 @@ tool_guid=missing_test_components_dict.get( 'tool_guid', '' ), tool_id=missing_test_components_dict.get( 'tool_id', '' ), tool_version=missing_test_components_dict.get( 'tool_version', '' ) ) - folder.missing_test_components.append( missing_test_component ) + missing_test_components_folder.missing_test_components.append( missing_test_component ) installation_error_dicts = tool_test_results_dict.get( 'installation_errors', {} ) if installation_error_dicts: current_repository_errors = installation_error_dicts.get( 'current_repository', [] ) @@ -1165,54 +1186,57 @@ containing_folder.installation_errors.append( installation_error_base_folder ) if current_repository_errors: folder_id += 1 - subfolder = Folder( id=folder_id, - key='current_repository_errors', - label='This repository', - parent=installation_error_base_folder ) + current_repository_folder = Folder( id=folder_id, + key='current_repository_errors', + label='This repository', + parent=installation_error_base_folder ) repository_error_id = 0 for repository_error_dict in current_repository_errors: repository_error_id += 1 - repository_installation_error = RepositoryInstallationError( id=repository_error_id, - tool_shed=repository_error_dict.get( 'tool_shed', '' ), - name=repository_error_dict.get( 'name', '' ), - owner=repository_error_dict.get( 'owner', '' ), - changeset_revision=repository_error_dict.get( 'changeset_revision', '' ), - error_message=repository_error_dict.get( 'error_message', '' ) ) - subfolder.current_repository_installation_errors.append( repository_installation_error ) - installation_error_base_folder.folders.append( subfolder ) + repository_installation_error = \ + RepositoryInstallationError( id=repository_error_id, + tool_shed=repository_error_dict.get( 'tool_shed', '' ), + name=repository_error_dict.get( 'name', '' ), + owner=repository_error_dict.get( 'owner', '' ), + changeset_revision=repository_error_dict.get( 'changeset_revision', '' ), + error_message=repository_error_dict.get( 'error_message', '' ) ) + current_repository_folder.current_repository_installation_errors.append( repository_installation_error ) + installation_error_base_folder.folders.append( current_repository_folder ) if repository_dependency_errors: folder_id += 1 - subfolder = Folder( id=folder_id, - key='repository_dependency_errors', - label='Repository dependencies', - parent=installation_error_base_folder ) + repository_dependencies_folder = Folder( id=folder_id, + key='repository_dependency_errors', + label='Repository dependencies', + parent=installation_error_base_folder ) repository_error_id = 0 for repository_error_dict in repository_dependency_errors: repository_error_id += 1 - repository_installation_error = RepositoryInstallationError( id=repository_error_id, - tool_shed=repository_error_dict.get( 'tool_shed', '' ), - name=repository_error_dict.get( 'name', '' ), - owner=repository_error_dict.get( 'owner', '' ), - changeset_revision=repository_error_dict.get( 'changeset_revision', '' ), - error_message=repository_error_dict.get( 'error_message', '' ) ) - subfolder.repository_installation_errors.append( repository_installation_error ) - installation_error_base_folder.folders.append( subfolder ) + repository_installation_error = \ + RepositoryInstallationError( id=repository_error_id, + tool_shed=repository_error_dict.get( 'tool_shed', '' ), + name=repository_error_dict.get( 'name', '' ), + owner=repository_error_dict.get( 'owner', '' ), + changeset_revision=repository_error_dict.get( 'changeset_revision', '' ), + error_message=repository_error_dict.get( 'error_message', '' ) ) + repository_dependencies_folder.repository_installation_errors.append( repository_installation_error ) + installation_error_base_folder.folders.append( repository_dependencies_folder ) if tool_dependency_errors: folder_id += 1 - subfolder = Folder( id=folder_id, - key='tool_dependency_errors', - label='Tool dependencies', - parent=installation_error_base_folder ) + tool_dependencies_folder = Folder( id=folder_id, + key='tool_dependency_errors', + label='Tool dependencies', + parent=installation_error_base_folder ) tool_dependency_error_id = 0 for tool_dependency_error_dict in tool_dependency_errors: tool_dependency_error_id += 1 - tool_dependency_installation_error = ToolDependencyInstallationError( id=tool_dependency_error_id, - type=tool_dependency_error_dict.get( 'type', '' ), - name=tool_dependency_error_dict.get( 'name', '' ), - version=tool_dependency_error_dict.get( 'version', '' ), - error_message=tool_dependency_error_dict.get( 'error_message', '' ) ) - subfolder.tool_dependency_installation_errors.append( tool_dependency_installation_error ) - installation_error_base_folder.folders.append( subfolder ) + tool_dependency_installation_error = \ + ToolDependencyInstallationError( id=tool_dependency_error_id, + type=tool_dependency_error_dict.get( 'type', '' ), + name=tool_dependency_error_dict.get( 'name', '' ), + version=tool_dependency_error_dict.get( 'version', '' ), + error_message=tool_dependency_error_dict.get( 'error_message', '' ) ) + tool_dependencies_folder.tool_dependency_installation_errors.append( tool_dependency_installation_error ) + installation_error_base_folder.folders.append( tool_dependencies_folder ) else: tool_test_results_root_folder = None return folder_id, tool_test_results_root_folder Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 10 new changesets
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

10 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fe2c12b2eb22/ Changeset: fe2c12b2eb22 User: jmchilton Date: 2013-12-02 02:07:03 Summary: Refactor directory_hash_id into its own module. Also add PEP-8 cleanup and unit tests. This eliminates explicit dependency between galaxy.objectstore and galaxy.model - with the ultimate goal of being able to utilize all object store functionality except dataset creation from a remote LWR instance without a database connection. Affected #: 4 files diff -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 -r fe2c12b2eb22a5cab876629593e91079e27f2492 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -29,6 +29,7 @@ from galaxy.util import asbool, is_multi_byte, nice_size, Params, restore_text, send_mail from galaxy.util.bunch import Bunch from galaxy.util.hash_util import new_secure_hash +from galaxy.util.directory_hash import directory_hash_id from galaxy.web.framework.helpers import to_unicode from galaxy.web.form_builder import (AddressField, CheckboxField, HistoryField, PasswordField, SelectField, TextArea, TextField, WorkflowField, @@ -4029,18 +4030,3 @@ self.repository_id = repository_id self.repository_path = repository_path self.version = version - -## ---- Utility methods ------------------------------------------------------- - -def directory_hash_id( id ): - s = str( id ) - l = len( s ) - # Shortcut -- ids 0-999 go under ../000/ - if l < 4: - return [ "000" ] - # Pad with zeros until a multiple of three - padded = ( ( 3 - len( s ) % 3 ) * "0" ) + s - # Drop the last three digits -- 1000 files per directory - padded = padded[:-3] - # Break into chunks of three - return [ padded[i*3:(i+1)*3] for i in range( len( padded ) // 3 ) ] diff -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 -r fe2c12b2eb22a5cab876629593e91079e27f2492 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -13,7 +13,7 @@ from galaxy import util from galaxy.exceptions import ObjectInvalid, ObjectNotFound from galaxy.jobs import Sleeper -from galaxy.model import directory_hash_id +from galaxy.util.directory_hash import directory_hash_id from galaxy.util.odict import odict from sqlalchemy.orm import object_session diff -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 -r fe2c12b2eb22a5cab876629593e91079e27f2492 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -12,7 +12,7 @@ from galaxy import util from galaxy.jobs import Sleeper -from galaxy.model import directory_hash_id +from galaxy.util.directory_hash import directory_hash_id from galaxy.objectstore import ObjectStore, convert_bytes from galaxy.exceptions import ObjectNotFound diff -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 -r fe2c12b2eb22a5cab876629593e91079e27f2492 lib/galaxy/util/directory_hash.py --- /dev/null +++ b/lib/galaxy/util/directory_hash.py @@ -0,0 +1,23 @@ + + +def directory_hash_id( id ): + """ + + >>> directory_hash_id( 100 ) + ['000'] + >>> directory_hash_id( "90000" ) + ['090'] + >>> directory_hash_id("777777777") + ['000', '777', '777'] + """ + s = str( id ) + l = len( s ) + # Shortcut -- ids 0-999 go under ../000/ + if l < 4: + return [ "000" ] + # Pad with zeros until a multiple of three + padded = ( ( 3 - len( s ) % 3 ) * "0" ) + s + # Drop the last three digits -- 1000 files per directory + padded = padded[:-3] + # Break into chunks of three + return [ padded[ i * 3 : (i + 1 ) * 3 ] for i in range( len( padded ) // 3 ) ] https://bitbucket.org/galaxy/galaxy-central/commits/433d5f4f5c66/ Changeset: 433d5f4f5c66 User: jmchilton Date: 2013-12-02 02:07:04 Summary: PEP-8 fixes for object store module. Affected #: 3 files diff -r fe2c12b2eb22a5cab876629593e91079e27f2492 -r 433d5f4f5c66c17701d84b08185ca2b733664d6b lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -358,7 +358,7 @@ def get_store_usage_percent(self): st = os.statvfs(self.file_path) - return (float(st.f_blocks - st.f_bavail)/st.f_blocks) * 100 + return ( float( st.f_blocks - st.f_bavail ) / st.f_blocks ) * 100 class CachingObjectStore(ObjectStore): @@ -428,7 +428,7 @@ return store.__getattribute__(method)(obj, **kwargs) if default_is_exception: raise default( 'objectstore, __call_method failed: %s on %s, kwargs: %s' - %( method, str( obj ), str( kwargs ) ) ) + % ( method, str( obj ), str( kwargs ) ) ) else: return default @@ -462,7 +462,7 @@ self.filesystem_monitor_thread.start() log.info("Filesystem space monitor started") - def __parse_distributed_config(self, config, config_xml = None): + def __parse_distributed_config(self, config, config_xml=None): if not config_xml: tree = util.parse_xml(self.distributed_config) root = tree.getroot() @@ -512,7 +512,7 @@ if pct > maxpct: new_weighted_backend_ids = filter(lambda x: x != id, new_weighted_backend_ids) self.weighted_backend_ids = new_weighted_backend_ids - self.sleeper.sleep(120) # Test free space every 2 minutes + self.sleeper.sleep(120) # Test free space every 2 minutes def create(self, obj, **kwargs): """ @@ -524,7 +524,7 @@ obj.object_store_id = random.choice(self.weighted_backend_ids) except IndexError: raise ObjectInvalid( 'objectstore.create, could not generate obj.object_store_id: %s, kwargs: %s' - %( str( obj ), str( kwargs ) ) ) + % ( str( obj ), str( kwargs ) ) ) object_session( obj ).add( obj ) object_session( obj ).flush() log.debug("Selected backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id)) @@ -538,7 +538,7 @@ return self.backends[object_store_id].__getattribute__(method)(obj, **kwargs) if default_is_exception: raise default( 'objectstore, __call_method failed: %s on %s, kwargs: %s' - %( method, str( obj ), str( kwargs ) ) ) + % ( method, str( obj ), str( kwargs ) ) ) else: return default @@ -625,6 +625,7 @@ else: log.error("Unrecognized object store definition: {0}".format(store)) + def local_extra_dirs( func ): """ A decorator for non-local plugins to utilize local directories for their extra_dirs (job_working_directory and temp). """ @@ -638,6 +639,7 @@ raise Exception( "Could not call DiskObjectStore's %s method, does your Object Store plugin inherit from DiskObjectStore?" % func.__name__ ) return wraps + def convert_bytes(bytes): """ A helper function used for pretty printing disk usage """ if bytes is None: diff -r fe2c12b2eb22a5cab876629593e91079e27f2492 -r 433d5f4f5c66c17701d84b08185ca2b733664d6b lib/galaxy/objectstore/rods.py --- a/lib/galaxy/objectstore/rods.py +++ b/lib/galaxy/objectstore/rods.py @@ -146,7 +146,7 @@ doi = irods.dataObjInp_t() doi.objPath = rods_path doi.createMode = 0640 - doi.dataSize = 0 # 0 actually means "unknown", although literally 0 would be preferable + doi.dataSize = 0 # 0 actually means "unknown", although literally 0 would be preferable irods.addKeyVal( doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource ) status = irods.rcDataObjCreate( self.rods_conn, doi ) assert status >= 0, 'create(): rcDataObjCreate() failed: %s: %s: %s' % ( rods_path, status, irods.strerror( status ) ) @@ -237,7 +237,7 @@ incoming_path = os.path.join( os.path.dirname( cached_path ), "__incoming_%s" % os.path.basename( cached_path ) ) doi = irods.dataObjInp_t() doi.objPath = self.__get_rods_path( obj, **kwargs ) - doi.dataSize = 0 # TODO: does this affect performance? should we get size? + doi.dataSize = 0 # TODO: does this affect performance? should we get size? doi.numThreads = 0 # TODO: might want to VERIFY_CHKSUM_KW log.debug( 'get_filename(): caching %s to %s', doi.objPath, incoming_path ) @@ -296,6 +296,7 @@ def get_store_usage_percent(self): return 0.0 + # monkeypatch an strerror method into the irods module def _rods_strerror( errno ): """ @@ -311,6 +312,7 @@ irods.strerror = _rods_strerror + def rods_connect(): """ A basic iRODS connection mechanism that connects using the current iRODS diff -r fe2c12b2eb22a5cab876629593e91079e27f2492 -r 433d5f4f5c66c17701d84b08185ca2b733664d6b lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -24,7 +24,7 @@ from boto.exception import S3ResponseError log = logging.getLogger( __name__ ) -logging.getLogger('boto').setLevel(logging.INFO) # Otherwise boto is quite noisy +logging.getLogger('boto').setLevel(logging.INFO) # Otherwise boto is quite noisy class S3ObjectStore(ObjectStore): @@ -82,7 +82,7 @@ raise def __cache_monitor(self): - time.sleep(2) # Wait for things to load before starting the monitor + time.sleep(2) # Wait for things to load before starting the monitor while self.running: total_size = 0 # Is this going to be too expensive of an operation to be done frequently? @@ -110,7 +110,7 @@ # For now, delete enough to leave at least 10% of the total cache free delete_this_much = total_size - cache_limit self.__clean_cache(file_list, delete_this_much) - self.sleeper.sleep(30) # Test cache size every 30 seconds? + self.sleeper.sleep(30) # Test cache size every 30 seconds? def __clean_cache(self, file_list, delete_this_much): """ Keep deleting files from the file_list until the size of the deleted @@ -154,7 +154,7 @@ log.debug("Using cloud object store with bucket '%s'" % bucket.name) return bucket except S3ResponseError: - log.debug("Could not get bucket '%s', attempt %s/5" % (bucket_name, i+1)) + log.debug("Could not get bucket '%s', attempt %s/5" % (bucket_name, i + 1)) time.sleep(2) # All the attempts have been exhausted and connection was not established, # raise error @@ -283,7 +283,7 @@ return True else: log.debug("Pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))) - self.transfer_progress = 0 # Reset transfer progress counter + self.transfer_progress = 0 # Reset transfer progress counter key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10) return True except S3ResponseError, ex: @@ -315,14 +315,14 @@ mb_size = os.path.getsize(source_file) / 1e6 #DBTODO Hack, refactor this logic. if mb_size < 60 or type(self) == SwiftObjectStore: - self.transfer_progress = 0 # Reset transfer progress counter + self.transfer_progress = 0 # Reset transfer progress counter key.set_contents_from_filename(source_file, reduced_redundancy=self.use_rr, cb=self._transfer_cb, num_cb=10) else: multipart_upload(self.bucket, key.name, source_file, mb_size, use_rr=self.use_rr) end_time = datetime.now() # print "+ Push ended at '%s'; %s bytes transfered in %ssec" % (end_time, os.path.getsize(source_file), end_time-start_time) - log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)" % (source_file, rel_path, os.path.getsize(source_file), end_time-start_time)) + log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)" % (source_file, rel_path, os.path.getsize(source_file), end_time - start_time)) return True else: log.error("Tried updating key '%s' from source file '%s', but source file does not exist." @@ -408,7 +408,7 @@ return bool(self.size(obj, **kwargs) > 0) else: raise ObjectNotFound( 'objectstore.empty, object does not exist: %s, kwargs: %s' - %( str( obj ), str( kwargs ) ) ) + % ( str( obj ), str( kwargs ) ) ) def size(self, obj, **kwargs): rel_path = self._construct_path(obj, **kwargs) @@ -484,7 +484,7 @@ return cache_path # Check if the file exists in persistent storage and, if it does, pull it into cache elif self.exists(obj, **kwargs): - if dir_only: # Directories do not get pulled into cache + if dir_only: # Directories do not get pulled into cache return cache_path else: if self._pull_into_cache(rel_path): @@ -494,7 +494,7 @@ # if dir_only: # return cache_path raise ObjectNotFound( 'objectstore.get_filename, no cache_path: %s, kwargs: %s' - %( str( obj ), str( kwargs ) ) ) + % ( str( obj ), str( kwargs ) ) ) # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path def update_from_file(self, obj, file_name=None, create=False, **kwargs): @@ -520,14 +520,14 @@ self._push_to_os(rel_path, source_file) else: raise ObjectNotFound( 'objectstore.update_from_file, object does not exist: %s, kwargs: %s' - %( str( obj ), str( kwargs ) ) ) + % ( str( obj ), str( kwargs ) ) ) def get_object_url(self, obj, **kwargs): if self.exists(obj, **kwargs): rel_path = self._construct_path(obj, **kwargs) try: key = Key(self.bucket, rel_path) - return key.generate_url(expires_in = 86400) # 24hrs + return key.generate_url(expires_in=86400) # 24hrs except S3ResponseError, ex: log.warning("Trouble generating URL for dataset '%s': %s" % (rel_path, ex)) return None @@ -552,4 +552,3 @@ port=self.port, calling_format=boto.s3.connection.OrdinaryCallingFormat(), path=self.conn_path) - https://bitbucket.org/galaxy/galaxy-central/commits/1f62ef450cd7/ Changeset: 1f62ef450cd7 User: jmchilton Date: 2013-12-02 02:07:04 Summary: Refactor jobs.Sleeper into its own module. This eliminates explicit dependency between galaxy.objectstore and galaxy.job - with the ultimate goal of being able to utilize all object store functionality except dataset creation from a remote LWR instance with minimal dependencies. Affected #: 6 files diff -r 433d5f4f5c66c17701d84b08185ca2b733664d6b -r 1f62ef450cd7c79af0de6a22f8c2b1c1b6cb9114 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -14,7 +14,6 @@ import shutil import subprocess import sys -import threading import traceback from galaxy import model, util from galaxy.datatypes import metadata @@ -39,21 +38,6 @@ # and should eventually become API'd TOOL_PROVIDED_JOB_METADATA_FILE = 'galaxy.json' -class Sleeper( object ): - """ - Provides a 'sleep' method that sleeps for a number of seconds *unless* - the notify method is called (from a different thread). - """ - def __init__( self ): - self.condition = threading.Condition() - def sleep( self, seconds ): - self.condition.acquire() - self.condition.wait( seconds ) - self.condition.release() - def wake( self ): - self.condition.acquire() - self.condition.notify() - self.condition.release() class JobDestination( Bunch ): """ diff -r 433d5f4f5c66c17701d84b08185ca2b733664d6b -r 1f62ef450cd7c79af0de6a22f8c2b1c1b6cb9114 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -11,7 +11,8 @@ from sqlalchemy.sql.expression import and_, or_, select, func from galaxy import model -from galaxy.jobs import Sleeper, JobWrapper, TaskWrapper, JobDestination +from galaxy.util.sleeper import Sleeper +from galaxy.jobs import JobWrapper, TaskWrapper, JobDestination log = logging.getLogger( __name__ ) diff -r 433d5f4f5c66c17701d84b08185ca2b733664d6b -r 1f62ef450cd7c79af0de6a22f8c2b1c1b6cb9114 lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -11,7 +11,8 @@ from Queue import Empty, Queue from galaxy import model -from galaxy.jobs import handler, JobWrapper, NoopQueue, Sleeper +from galaxy.util.sleeper import Sleeper +from galaxy.jobs import handler, JobWrapper, NoopQueue from galaxy.util.json import from_json_string log = logging.getLogger( __name__ ) diff -r 433d5f4f5c66c17701d84b08185ca2b733664d6b -r 1f62ef450cd7c79af0de6a22f8c2b1c1b6cb9114 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -12,7 +12,7 @@ from galaxy import util from galaxy.exceptions import ObjectInvalid, ObjectNotFound -from galaxy.jobs import Sleeper +from galaxy.util.sleeper import Sleeper from galaxy.util.directory_hash import directory_hash_id from galaxy.util.odict import odict diff -r 433d5f4f5c66c17701d84b08185ca2b733664d6b -r 1f62ef450cd7c79af0de6a22f8c2b1c1b6cb9114 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -11,7 +11,7 @@ from datetime import datetime from galaxy import util -from galaxy.jobs import Sleeper +from galaxy.util.sleeper import Sleeper from galaxy.util.directory_hash import directory_hash_id from galaxy.objectstore import ObjectStore, convert_bytes from galaxy.exceptions import ObjectNotFound diff -r 433d5f4f5c66c17701d84b08185ca2b733664d6b -r 1f62ef450cd7c79af0de6a22f8c2b1c1b6cb9114 lib/galaxy/util/sleeper.py --- /dev/null +++ b/lib/galaxy/util/sleeper.py @@ -0,0 +1,22 @@ +import threading + + +class Sleeper( object ): + """ + Provides a 'sleep' method that sleeps for a number of seconds *unless* + the notify method is called (from a different thread). + """ + def __init__( self ): + self.condition = threading.Condition() + + def sleep( self, seconds ): + # Should this be in a try/finally block? -John + self.condition.acquire() + self.condition.wait( seconds ) + self.condition.release() + + def wake( self ): + # Should this be in a try/finally block? -John + self.condition.acquire() + self.condition.notify() + self.condition.release() https://bitbucket.org/galaxy/galaxy-central/commits/b78fc1c8b14e/ Changeset: b78fc1c8b14e User: jmchilton Date: 2013-12-02 02:07:04 Summary: More work on objectstore dependencies. Be explicit about what in galaxy.util is being used, don't fail if galaxy.eggs is unavailable - assume the actual dependencies will be there (boto and rods) if not fail just a little later. If nothing else, this should fix some failing buildbot tests (nosetests records a failure if it cannot import a file and it cannot import the s3 or irods object store files because of these imports). Affected #: 4 files diff -r 1f62ef450cd7c79af0de6a22f8c2b1c1b6cb9114 -r b78fc1c8b14e7926d3551f5a676d107fc0a4ed89 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -10,7 +10,7 @@ import logging import threading -from galaxy import util +from galaxy.util import umask_fix_perms, parse_xml, force_symlink from galaxy.exceptions import ObjectInvalid, ObjectNotFound from galaxy.util.sleeper import Sleeper from galaxy.util.directory_hash import directory_hash_id @@ -291,7 +291,7 @@ # Create the file if it does not exist if not dir_only: open(path, 'w').close() - util.umask_fix_perms(path, self.config.umask, 0666) + umask_fix_perms(path, self.config.umask, 0666) def empty(self, obj, **kwargs): return os.path.getsize(self.get_filename(obj, **kwargs)) == 0 @@ -345,7 +345,7 @@ if file_name and self.exists(obj, **kwargs): try: if preserve_symlinks and os.path.islink( file_name ): - util.force_symlink( os.readlink( file_name ), self.get_filename( obj, **kwargs ) ) + force_symlink( os.readlink( file_name ), self.get_filename( obj, **kwargs ) ) else: shutil.copy( file_name, self.get_filename( obj, **kwargs ) ) except IOError, ex: @@ -464,7 +464,7 @@ def __parse_distributed_config(self, config, config_xml=None): if not config_xml: - tree = util.parse_xml(self.distributed_config) + tree = parse_xml(self.distributed_config) root = tree.getroot() log.debug('Loading backends for distributed object store from %s' % self.distributed_config) else: @@ -598,7 +598,7 @@ # This is a top level invocation of build_object_store_from_config, and # we have an object_store_conf.xml -- read the .xml and build # accordingly - tree = util.parse_xml(config.object_store_config_file) + tree = parse_xml(config.object_store_config_file) root = tree.getroot() store = root.get('type') config_xml = root diff -r 1f62ef450cd7c79af0de6a22f8c2b1c1b6cb9114 -r b78fc1c8b14e7926d3551f5a676d107fc0a4ed89 lib/galaxy/objectstore/rods.py --- a/lib/galaxy/objectstore/rods.py +++ b/lib/galaxy/objectstore/rods.py @@ -15,9 +15,14 @@ from galaxy.objectstore import DiskObjectStore, ObjectStore, local_extra_dirs from galaxy.exceptions import ObjectNotFound -import galaxy.eggs -galaxy.eggs.require( 'PyRods' ) -import irods +try: + import galaxy.eggs + galaxy.eggs.require( 'PyRods' ) + import irods +except ImportError: + irods = None + +NO_PYRODS_ERROR_MESSAGE = "IRODS object store configured, but no PyRods dependency available. Please install and properly configure PyRods or modify object store configuration." log = logging.getLogger( __name__ ) @@ -27,6 +32,8 @@ Galaxy object store based on iRODS """ def __init__( self, config, file_path=None, extra_dirs=None ): + if irods is None: + raise Exception(NO_PYRODS_ERROR_MESSAGE) super( IRODSObjectStore, self ).__init__( config, file_path=file_path, extra_dirs=extra_dirs ) self.cache_path = config.object_store_cache_path self.default_resource = config.irods_default_resource or None @@ -310,7 +317,8 @@ irods.__rods_strerror_map[ v ] = name return irods.__rods_strerror_map.get( errno, 'GALAXY_NO_ERRNO_MAPPING_FOUND' ) -irods.strerror = _rods_strerror +if irods is not None: + irods.strerror = _rods_strerror def rods_connect(): diff -r 1f62ef450cd7c79af0de6a22f8c2b1c1b6cb9114 -r b78fc1c8b14e7926d3551f5a676d107fc0a4ed89 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -10,7 +10,7 @@ import subprocess from datetime import datetime -from galaxy import util +from galaxy.util import umask_fix_perms from galaxy.util.sleeper import Sleeper from galaxy.util.directory_hash import directory_hash_id from galaxy.objectstore import ObjectStore, convert_bytes @@ -18,10 +18,16 @@ import multiprocessing from galaxy.objectstore.s3_multipart_upload import multipart_upload -import boto -from boto.s3.key import Key -from boto.s3.connection import S3Connection -from boto.exception import S3ResponseError +try: + import boto + from boto.s3.key import Key + from boto.s3.connection import S3Connection + from boto.exception import S3ResponseError +except ImportError: + boto = None + +NO_BOTO_ERROR_MESSAGE = "S3/Swift object store configured, but no boto dependency available. Please install and properly configure boto or modify object store configuration." + log = logging.getLogger( __name__ ) logging.getLogger('boto').setLevel(logging.INFO) # Otherwise boto is quite noisy @@ -34,6 +40,8 @@ Galaxy and S3. """ def __init__(self, config, config_xml): + if boto is None: + raise Exception(NO_BOTO_ERROR_MESSAGE) super(S3ObjectStore, self).__init__(config, config_xml) self.config = config self.staging_path = self.config.file_path @@ -163,13 +171,13 @@ def _fix_permissions(self, rel_path): """ Set permissions on rel_path""" for basedir, dirs, files in os.walk(rel_path): - util.umask_fix_perms(basedir, self.config.umask, 0777, self.config.gid) + umask_fix_perms(basedir, self.config.umask, 0777, self.config.gid) for f in files: path = os.path.join(basedir, f) # Ignore symlinks if os.path.islink(path): continue - util.umask_fix_perms( path, self.config.umask, 0666, self.config.gid ) + umask_fix_perms( path, self.config.umask, 0666, self.config.gid ) def _construct_path(self, obj, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, **kwargs): rel_path = os.path.join(*directory_hash_id(obj.id)) diff -r 1f62ef450cd7c79af0de6a22f8c2b1c1b6cb9114 -r b78fc1c8b14e7926d3551f5a676d107fc0a4ed89 lib/galaxy/objectstore/s3_multipart_upload.py --- a/lib/galaxy/objectstore/s3_multipart_upload.py +++ b/lib/galaxy/objectstore/s3_multipart_upload.py @@ -4,10 +4,8 @@ This parallelizes the task over available cores using multiprocessing. Code mostly taken form CloudBioLinux. """ -from __future__ import with_statement import os -import sys import glob import subprocess import contextlib @@ -16,10 +14,17 @@ import multiprocessing from multiprocessing.pool import IMapIterator -from galaxy import eggs -eggs.require('boto') +try: + from galaxy import eggs + eggs.require('boto') +except ImportError: + pass -import boto +try: + import boto +except ImportError: + boto = None + def map_wrap(f): @functools.wraps(f) https://bitbucket.org/galaxy/galaxy-central/commits/a03f4f2f46dd/ Changeset: a03f4f2f46dd User: jmchilton Date: 2013-12-02 02:07:04 Summary: Use relative imports in objectstore code. Goal is to enable the whole module to be placed in lwr.objectstore. Affected #: 3 files diff -r b78fc1c8b14e7926d3551f5a676d107fc0a4ed89 -r a03f4f2f46dd783bd183def7ade25d0e10017ced lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -610,17 +610,17 @@ if store == 'disk': return DiskObjectStore(config=config, config_xml=config_xml) elif store == 's3': - from galaxy.objectstore.s3 import S3ObjectStore + from .s3 import S3ObjectStore return S3ObjectStore(config=config, config_xml=config_xml) elif store == 'swift': - from galaxy.objectstore.s3 import SwiftObjectStore + from .s3 import SwiftObjectStore return SwiftObjectStore(config=config, config_xml=config_xml) elif store == 'distributed': return DistributedObjectStore(config=config, fsmon=fsmon, config_xml=config_xml) elif store == 'hierarchical': return HierarchicalObjectStore(config=config, config_xml=config_xml) elif store == 'irods': - from galaxy.objectstore.rods import IRODSObjectStore + from .rods import IRODSObjectStore return IRODSObjectStore(config=config, config_xml=config_xml) else: log.error("Unrecognized object store definition: {0}".format(store)) diff -r b78fc1c8b14e7926d3551f5a676d107fc0a4ed89 -r a03f4f2f46dd783bd183def7ade25d0e10017ced lib/galaxy/objectstore/rods.py --- a/lib/galaxy/objectstore/rods.py +++ b/lib/galaxy/objectstore/rods.py @@ -12,8 +12,8 @@ from posixpath import basename as path_basename from posixpath import dirname as path_dirname -from galaxy.objectstore import DiskObjectStore, ObjectStore, local_extra_dirs from galaxy.exceptions import ObjectNotFound +from ..objectstore import DiskObjectStore, ObjectStore, local_extra_dirs try: import galaxy.eggs diff -r b78fc1c8b14e7926d3551f5a676d107fc0a4ed89 -r a03f4f2f46dd783bd183def7ade25d0e10017ced lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -13,11 +13,11 @@ from galaxy.util import umask_fix_perms from galaxy.util.sleeper import Sleeper from galaxy.util.directory_hash import directory_hash_id -from galaxy.objectstore import ObjectStore, convert_bytes +from ..objectstore import ObjectStore, convert_bytes from galaxy.exceptions import ObjectNotFound import multiprocessing -from galaxy.objectstore.s3_multipart_upload import multipart_upload +from .s3_multipart_upload import multipart_upload try: import boto from boto.s3.key import Key @@ -28,7 +28,6 @@ NO_BOTO_ERROR_MESSAGE = "S3/Swift object store configured, but no boto dependency available. Please install and properly configure boto or modify object store configuration." - log = logging.getLogger( __name__ ) logging.getLogger('boto').setLevel(logging.INFO) # Otherwise boto is quite noisy https://bitbucket.org/galaxy/galaxy-central/commits/10701b684e73/ Changeset: 10701b684e73 User: jmchilton Date: 2013-12-02 02:07:04 Summary: Make sqlalchemy dependency in object store optional unless create is used. Affected #: 1 file diff -r a03f4f2f46dd783bd183def7ade25d0e10017ced -r 10701b684e73af78f9688ded379e82b3417c86bf lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -15,8 +15,12 @@ from galaxy.util.sleeper import Sleeper from galaxy.util.directory_hash import directory_hash_id from galaxy.util.odict import odict +try: + from sqlalchemy.orm import object_session +except ImportError: + object_session = None -from sqlalchemy.orm import object_session +NO_SESSION_ERROR_MESSAGE = "Attempted to 'create' object store entity in configuration with no database session present." log = logging.getLogger( __name__ ) @@ -525,8 +529,7 @@ except IndexError: raise ObjectInvalid( 'objectstore.create, could not generate obj.object_store_id: %s, kwargs: %s' % ( str( obj ), str( kwargs ) ) ) - object_session( obj ).add( obj ) - object_session( obj ).flush() + create_object_in_session( obj ) log.debug("Selected backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id)) else: log.debug("Using preferred backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id)) @@ -554,8 +557,7 @@ if store.exists(obj, **kwargs): log.warning('%s object with ID %s found in backend object store with ID %s' % (obj.__class__.__name__, obj.id, id)) obj.object_store_id = id - object_session( obj ).add( obj ) - object_session( obj ).flush() + create_object_in_session( obj ) return id return None @@ -661,3 +663,12 @@ else: size = '%.2fb' % bytes return size + + +def create_object_in_session( obj ): + session = object_session( obj ) if object_session is not None else None + if session is not None: + object_session( obj ).add( obj ) + object_session( obj ).flush() + else: + raise Exception( NO_SESSION_ERROR_MESSAGE ) https://bitbucket.org/galaxy/galaxy-central/commits/1ba3ef72b736/ Changeset: 1ba3ef72b736 User: jmchilton Date: 2013-12-02 02:07:04 Summary: Update objectstore XML parsing to stdlib's ElementTree implementation. Eliminates dependency on older elementtree egg. Affected #: 1 file diff -r 10701b684e73af78f9688ded379e82b3417c86bf -r 1ba3ef72b7364678ab87d95412164eee89f8913e lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -9,8 +9,9 @@ import shutil import logging import threading +from xml.etree import ElementTree -from galaxy.util import umask_fix_perms, parse_xml, force_symlink +from galaxy.util import umask_fix_perms, force_symlink from galaxy.exceptions import ObjectInvalid, ObjectNotFound from galaxy.util.sleeper import Sleeper from galaxy.util.directory_hash import directory_hash_id @@ -206,7 +207,7 @@ self.extra_dirs['job_work'] = config.job_working_directory self.extra_dirs['temp'] = config.new_file_path #The new config_xml overrides universe settings. - if config_xml: + if config_xml is not None: for e in config_xml: if e.tag == 'files_dir': self.file_path = e.get('path') @@ -294,7 +295,7 @@ os.makedirs(dir) # Create the file if it does not exist if not dir_only: - open(path, 'w').close() + open(path, 'w').close() # Should be rb? umask_fix_perms(path, self.config.umask, 0666) def empty(self, obj, **kwargs): @@ -324,7 +325,7 @@ return False def get_data(self, obj, start=0, count=-1, **kwargs): - data_file = open(self.get_filename(obj, **kwargs), 'r') + data_file = open(self.get_filename(obj, **kwargs), 'r') # Should be rb? data_file.seek(start) content = data_file.read(count) data_file.close() @@ -446,7 +447,7 @@ def __init__(self, config, config_xml=None, fsmon=False): super(DistributedObjectStore, self).__init__(config, config_xml=config_xml) - if not config_xml: + if config_xml is None: self.distributed_config = config.distributed_object_store_config_file assert self.distributed_config is not None, "distributed object store ('object_store = distributed') " \ "requires a config file, please set one in " \ @@ -467,9 +468,8 @@ log.info("Filesystem space monitor started") def __parse_distributed_config(self, config, config_xml=None): - if not config_xml: - tree = parse_xml(self.distributed_config) - root = tree.getroot() + if config_xml is None: + root = ElementTree.parse(self.distributed_config).getroot() log.debug('Loading backends for distributed object store from %s' % self.distributed_config) else: root = config_xml.find('backends') @@ -596,15 +596,14 @@ Depending on the configuration setting, invoke the appropriate object store """ - if not config_xml and config.object_store_config_file: + if config_xml is None and config.object_store_config_file: # This is a top level invocation of build_object_store_from_config, and # we have an object_store_conf.xml -- read the .xml and build # accordingly - tree = parse_xml(config.object_store_config_file) - root = tree.getroot() + root = ElementTree.parse(config.object_store_config_file).getroot() store = root.get('type') config_xml = root - elif config_xml: + elif config_xml is not None: store = config_xml.get('type') else: store = config.object_store https://bitbucket.org/galaxy/galaxy-central/commits/a194847d84d3/ Changeset: a194847d84d3 User: jmchilton Date: 2013-12-02 02:07:04 Summary: Add test cases for some basic object store types. Namely tests for disk, hierarchical, and distributed stores - as well parsing. Affected #: 1 file diff -r 1ba3ef72b7364678ab87d95412164eee89f8913e -r a194847d84d373cd7efdb581819115e7303e0568 test/unit/test_objectstore.py --- /dev/null +++ b/test/unit/test_objectstore.py @@ -0,0 +1,210 @@ +import os +from shutil import rmtree +from string import Template +from tempfile import mkdtemp +try: + from galaxy import objectstore +except ImportError: + from lwr import objectstore +from contextlib import contextmanager + +DISK_TEST_CONFIG = """<?xml version="1.0"?> +<object_store type="disk"> + <files_dir path="${temp_directory}/files1"/> + <extra_dir type="temp" path="${temp_directory}/tmp1"/> + <extra_dir type="job_work" path="${temp_directory}/job_working_directory1"/> +</object_store> +""" + + +def test_disk_store(): + with TestConfig(DISK_TEST_CONFIG) as (directory, object_store): + # Test no dataset with id 1 exists. + absent_dataset = MockDataset(1) + assert not object_store.exists(absent_dataset) + + # Write empty dataset 2 in second backend, ensure it is empty and + # exists. + empty_dataset = MockDataset(2) + directory.write(b"", "files1/000/dataset_2.dat") + assert object_store.exists(empty_dataset) + assert object_store.empty(empty_dataset) + + # Write non-empty dataset in backend 1, test it is not emtpy & exists. + hello_world_dataset = MockDataset(3) + directory.write(b"Hello World!", "files1/000/dataset_3.dat") + assert object_store.exists(hello_world_dataset) + assert not object_store.empty(hello_world_dataset) + + # Test get_data + data = object_store.get_data(hello_world_dataset) + assert data == b"Hello World!" + + data = object_store.get_data(hello_world_dataset, start=1, count=6) + assert data == b"ello W" + + # Test Size + + # Test absent and empty datasets yield size of 0. + assert object_store.size(absent_dataset) == 0 + assert object_store.size(empty_dataset) == 0 + # Elsewise + assert object_store.size(hello_world_dataset) > 0 # Should this always be the number of bytes? + + # Test percent used (to some degree) + percent_store_used = object_store.get_store_usage_percent() + assert percent_store_used > 0.0 + assert percent_store_used < 100.0 + + # Test update_from_file test + output_dataset = MockDataset(4) + output_real_path = os.path.join(directory.temp_directory, "files1", "000", "dataset_4.dat") + assert not os.path.exists(output_real_path) + output_working_path = directory.write(b"NEW CONTENTS", "job_working_directory1/example_output") + object_store.update_from_file(output_dataset, file_name=output_working_path, create=True) + assert os.path.exists(output_real_path) + + # Test delete + to_delete_dataset = MockDataset(5) + to_delete_real_path = directory.write(b"content to be deleted!", "files1/000/dataset_5.dat") + assert object_store.exists(to_delete_dataset) + assert object_store.delete(to_delete_dataset) + assert not object_store.exists(to_delete_dataset) + assert not os.path.exists(to_delete_real_path) + + +HIERARCHICAL_TEST_CONFIG = """<?xml version="1.0"?> +<object_store type="hierarchical"> + <backends> + <backend id="files1" type="disk" weight="1" order="0"> + <files_dir path="${temp_directory}/files1"/> + <extra_dir type="temp" path="${temp_directory}/tmp1"/> + <extra_dir type="job_work" path="${temp_directory}/job_working_directory1"/> + </backend> + <backend id="files2" type="disk" weight="1" order="1"> + <files_dir path="${temp_directory}/files2"/> + <extra_dir type="temp" path="${temp_directory}/tmp2"/> + <extra_dir type="job_work" path="${temp_directory}/job_working_directory2"/> + </backend> + </backends> +</object_store> +""" + + +def test_hierarchical_store(): + with TestConfig(HIERARCHICAL_TEST_CONFIG) as (directory, object_store): + + # Test no dataset with id 1 exists. + assert not object_store.exists(MockDataset(1)) + + # Write empty dataset 2 in second backend, ensure it is empty and + # exists. + directory.write("", "files2/000/dataset_2.dat") + assert object_store.exists(MockDataset(2)) + assert object_store.empty(MockDataset(2)) + + # Write non-empty dataset in backend 1, test it is not emtpy & exists. + directory.write("Hello World!", "files1/000/dataset_3.dat") + assert object_store.exists(MockDataset(3)) + assert not object_store.empty(MockDataset(3)) + + # Assert creation always happens in first backend. + for i in range(100): + dataset = MockDataset(100 + i) + object_store.create(dataset) + assert object_store.get_filename(dataset).find("files1") > 0 + + +DISTRIBUTED_TEST_CONFIG = """<?xml version="1.0"?> +<object_store type="distributed"> + <backends> + <backend id="files1" type="disk" weight="2" order="0"> + <files_dir path="${temp_directory}/files1"/> + <extra_dir type="temp" path="${temp_directory}/tmp1"/> + <extra_dir type="job_work" path="${temp_directory}/job_working_directory1"/> + </backend> + <backend id="files2" type="disk" weight="1" order="1"> + <files_dir path="${temp_directory}/files2"/> + <extra_dir type="temp" path="${temp_directory}/tmp2"/> + <extra_dir type="job_work" path="${temp_directory}/job_working_directory2"/> + </backend> + </backends> +</object_store> +""" + + +def test_distributed_store(): + with TestConfig(DISTRIBUTED_TEST_CONFIG) as (directory, object_store): + with __stubbed_persistence() as persisted_ids: + for i in range(100): + dataset = MockDataset(100 + i) + object_store.create(dataset) + + ## Test distributes datasets between backends according to weights + backend_1_count = len([v for v in persisted_ids.values() if v == "files1"]) + backend_2_count = len([v for v in persisted_ids.values() if v == "files2"]) + + assert backend_1_count > 0 + assert backend_2_count > 0 + assert backend_1_count > backend_2_count + + +class TestConfig(object): + def __init__(self, config_xml): + self.temp_directory = mkdtemp() + self.write(config_xml, "store.xml") + config = MockConfig(self.temp_directory) + self.object_store = objectstore.build_object_store_from_config(config) + + def __enter__(self): + return self, self.object_store + + def __exit__(self, type, value, tb): + rmtree(self.temp_directory) + + def write(self, contents, name): + path = os.path.join(self.temp_directory, name) + directory = os.path.dirname(path) + if not os.path.exists(directory): + os.makedirs(directory) + expanded_contents = Template(contents).safe_substitute(temp_directory=self.temp_directory) + open(path, "w").write(expanded_contents) + return path + + +class MockConfig(object): + + def __init__(self, temp_directory): + self.file_path = temp_directory + self.object_store_config_file = os.path.join(temp_directory, "store.xml") + self.object_store_check_old_style = False + self.job_working_directory = temp_directory + self.new_file_path = temp_directory + self.umask = 0000 + + +class MockDataset(object): + + def __init__(self, id): + self.id = id + self.object_store_id = None + + +## Poor man's mocking. Need to get a real mocking library as real Galaxy development +## dependnecy. +PERSIST_METHOD_NAME = "create_object_in_session" + + +@contextmanager +def __stubbed_persistence(): + real_method = getattr(objectstore, PERSIST_METHOD_NAME) + try: + persisted_ids = {} + + def persist(object): + persisted_ids[object.id] = object.object_store_id + setattr(objectstore, PERSIST_METHOD_NAME, persist) + yield persisted_ids + + finally: + setattr(objectstore, PERSIST_METHOD_NAME, real_method) https://bitbucket.org/galaxy/galaxy-central/commits/5c62540e3f59/ Changeset: 5c62540e3f59 User: jmchilton Date: 2013-12-02 02:07:04 Summary: Add an LWR object store implementation. This changeset implements an object store implementation that delegates to a concrete remote object store instance via an LWR server. Can utilize existing LWR security mechanisms and multiple transport options. Updates the Galaxy LWR client through LWR changeset 2333f57. This changeset contains no tests for this new implementation, but the LWR contains the same code along with an integration test that spins up a temp LWR to test against - this test case demonstrating the lwr object store client and server can be found here : https://bitbucket.org/jmchilton/lwr/src/default/test/lwr_objectstore_test.py. Affected #: 4 files diff -r a194847d84d373cd7efdb581819115e7303e0568 -r 5c62540e3f5999fe70b3eeff73bee8cce5aa24c3 lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -50,6 +50,7 @@ return "No remote output found for path %s" % self.path +# TODO: Rename to job client. class Client(object): """ Objects of this client class perform low-level communication with a remote LWR server. @@ -326,3 +327,55 @@ @parseJson() def file_available(self, path): return self._raw_execute("file_available", {"path": path}) + + +class ObjectStoreClient(object): + + def __init__(self, lwr_interface): + self.lwr_interface = lwr_interface + + @parseJson() + def exists(self, **kwds): + return self._raw_execute("object_store_exists", args=self.__data(**kwds)) + + @parseJson() + def file_ready(self, **kwds): + return self._raw_execute("object_store_file_ready", args=self.__data(**kwds)) + + @parseJson() + def create(self, **kwds): + return self._raw_execute("object_store_create", args=self.__data(**kwds)) + + @parseJson() + def empty(self, **kwds): + return self._raw_execute("object_store_empty", args=self.__data(**kwds)) + + @parseJson() + def size(self, **kwds): + return self._raw_execute("object_store_size", args=self.__data(**kwds)) + + @parseJson() + def delete(self, **kwds): + return self._raw_execute("object_store_delete", args=self.__data(**kwds)) + + @parseJson() + def get_data(self, **kwds): + return self._raw_execute("object_store_get_data", args=self.__data(**kwds)) + + @parseJson() + def get_filename(self, **kwds): + return self._raw_execute("object_store_get_filename", args=self.__data(**kwds)) + + @parseJson() + def update_from_file(self, **kwds): + return self._raw_execute("object_store_update_from_file", args=self.__data(**kwds)) + + @parseJson() + def get_store_usage_percent(self): + return self._raw_execute("object_store_get_store_usage_percent", args={}) + + def __data(self, **kwds): + return kwds + + def _raw_execute(self, command, args={}): + return self.lwr_interface.execute(command, args, data=None, input_path=None, output_path=None) diff -r a194847d84d373cd7efdb581819115e7303e0568 -r 5c62540e3f5999fe70b3eeff73bee8cce5aa24c3 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -19,6 +19,7 @@ from galaxy.util import unicodify as text_type from .client import Client, InputCachingClient +from .client import ObjectStoreClient from .transport import get_transport from .util import TransferEventManager from .destination import url_to_destination_params @@ -74,6 +75,26 @@ return destination_params +class ObjectStoreClientManager(object): + + def __init__(self, **kwds): + if 'object_store' in kwds: + self.interface_class = LocalLwrInterface + self.interface_args = dict(object_store=kwds['object_store']) + else: + self.interface_class = HttpLwrInterface + transport_type = kwds.get('transport_type', None) + transport = get_transport(transport_type) + self.interface_args = dict(transport=transport) + self.extra_client_kwds = {} + + def get_client(self, client_params): + interface_class = self.interface_class + interface_args = dict(destination_params=client_params, **self.interface_args) + interface = interface_class(**interface_args) + return ObjectStoreClient(interface) + + class JobManagerInteface(object): """ Abstract base class describes how client communicates with remote job @@ -114,9 +135,10 @@ class LocalLwrInterface(object): - def __init__(self, destination_params, job_manager, file_cache): + def __init__(self, destination_params, job_manager=None, file_cache=None, object_store=None): self.job_manager = job_manager self.file_cache = file_cache + self.object_store = object_store def __app_args(self): ## Arguments that would be specified from LwrApp if running @@ -124,6 +146,7 @@ return { 'manager': self.job_manager, 'file_cache': self.file_cache, + 'object_store': self.object_store, 'ip': None } @@ -204,4 +227,4 @@ int_val = int(val) return int_val -__all__ = [ClientManager, HttpLwrInterface] +__all__ = [ClientManager, ObjectStoreClientManager, HttpLwrInterface] diff -r a194847d84d373cd7efdb581819115e7303e0568 -r 5c62540e3f5999fe70b3eeff73bee8cce5aa24c3 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -623,6 +623,9 @@ elif store == 'irods': from .rods import IRODSObjectStore return IRODSObjectStore(config=config, config_xml=config_xml) + elif store == 'lwr': + from .lwr import LwrObjectStore + return LwrObjectStore(config=config, config_xml=config_xml) else: log.error("Unrecognized object store definition: {0}".format(store)) diff -r a194847d84d373cd7efdb581819115e7303e0568 -r 5c62540e3f5999fe70b3eeff73bee8cce5aa24c3 lib/galaxy/objectstore/lwr.py --- /dev/null +++ b/lib/galaxy/objectstore/lwr.py @@ -0,0 +1,76 @@ +from __future__ import absolute_import # Need to import lwr_client absolutely. +from ..objectstore import ObjectStore +try: + from galaxy.jobs.runners.lwr_client.manager import ObjectStoreClientManager +except ImportError: + from lwr.lwr_client.manager import ObjectStoreClientManager + + +class LwrObjectStore(ObjectStore): + """ + Object store implementation that delegates to a remote LWR server. + + This may be more aspirational than practical for now, it would be good to + Galaxy to a point that a handler thread could be setup that doesn't attempt + to access the disk files returned by a (this) object store - just passing + them along to the LWR unmodified. That modification - along with this + implementation and LWR job destinations would then allow Galaxy to fully + manage jobs on remote servers with completely different mount points. + + This implementation should be considered beta and may be dropped from + Galaxy at some future point or significantly modified. + """ + + def __init__(self, config, config_xml): + self.lwr_client = self.__build_lwr_client(config_xml) + + def exists(self, obj, **kwds): + return self.lwr_client.exists(**self.__build_kwds(obj, **kwds)) + + def file_ready(self, obj, **kwds): + return self.lwr_client.file_ready(**self.__build_kwds(obj, **kwds)) + + def create(self, obj, **kwds): + return self.lwr_client.create(**self.__build_kwds(obj, **kwds)) + + def empty(self, obj, **kwds): + return self.lwr_client.empty(**self.__build_kwds(obj, **kwds)) + + def size(self, obj, **kwds): + return self.lwr_client.size(**self.__build_kwds(obj, **kwds)) + + def delete(self, obj, **kwds): + return self.lwr_client.delete(**self.__build_kwds(obj, **kwds)) + + # TODO: Optimize get_data. + def get_data(self, obj, **kwds): + return self.lwr_client.get_data(**self.__build_kwds(obj, **kwds)) + + def get_filename(self, obj, **kwds): + return self.lwr_client.get_filename(**self.__build_kwds(obj, **kwds)) + + def update_from_file(self, obj, **kwds): + return self.lwr_client.update_from_file(**self.__build_kwds(obj, **kwds)) + + def get_store_usage_percent(self): + return self.lwr_client.get_store_usage_percent() + + def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): + return None + + def __build_kwds(self, obj, **kwds): + kwds['object_id'] = obj.id + return kwds + pass + + def __build_lwr_client(self, config_xml): + url = config_xml.get("url") + private_token = config_xml.get("private_token", None) + transport = config_xml.get("transport", None) + manager_options = dict(transport=transport) + client_options = dict(url=url, private_token=private_token) + lwr_client = ObjectStoreClientManager(**manager_options).get_client(client_options) + return lwr_client + + def shutdown(self): + pass https://bitbucket.org/galaxy/galaxy-central/commits/a540510a3091/ Changeset: a540510a3091 User: dannon Date: 2013-12-03 17:12:57 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #269) Object Store dependency refactoring, testing, and added LWR implementation. Affected #: 14 files diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -14,7 +14,6 @@ import shutil import subprocess import sys -import threading import traceback from galaxy import model, util from galaxy.datatypes import metadata @@ -39,21 +38,6 @@ # and should eventually become API'd TOOL_PROVIDED_JOB_METADATA_FILE = 'galaxy.json' -class Sleeper( object ): - """ - Provides a 'sleep' method that sleeps for a number of seconds *unless* - the notify method is called (from a different thread). - """ - def __init__( self ): - self.condition = threading.Condition() - def sleep( self, seconds ): - self.condition.acquire() - self.condition.wait( seconds ) - self.condition.release() - def wake( self ): - self.condition.acquire() - self.condition.notify() - self.condition.release() class JobDestination( Bunch ): """ diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -11,7 +11,8 @@ from sqlalchemy.sql.expression import and_, or_, select, func from galaxy import model -from galaxy.jobs import Sleeper, JobWrapper, TaskWrapper, JobDestination +from galaxy.util.sleeper import Sleeper +from galaxy.jobs import JobWrapper, TaskWrapper, JobDestination log = logging.getLogger( __name__ ) diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -11,7 +11,8 @@ from Queue import Empty, Queue from galaxy import model -from galaxy.jobs import handler, JobWrapper, NoopQueue, Sleeper +from galaxy.util.sleeper import Sleeper +from galaxy.jobs import handler, JobWrapper, NoopQueue from galaxy.util.json import from_json_string log = logging.getLogger( __name__ ) diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -50,6 +50,7 @@ return "No remote output found for path %s" % self.path +# TODO: Rename to job client. class Client(object): """ Objects of this client class perform low-level communication with a remote LWR server. @@ -326,3 +327,55 @@ @parseJson() def file_available(self, path): return self._raw_execute("file_available", {"path": path}) + + +class ObjectStoreClient(object): + + def __init__(self, lwr_interface): + self.lwr_interface = lwr_interface + + @parseJson() + def exists(self, **kwds): + return self._raw_execute("object_store_exists", args=self.__data(**kwds)) + + @parseJson() + def file_ready(self, **kwds): + return self._raw_execute("object_store_file_ready", args=self.__data(**kwds)) + + @parseJson() + def create(self, **kwds): + return self._raw_execute("object_store_create", args=self.__data(**kwds)) + + @parseJson() + def empty(self, **kwds): + return self._raw_execute("object_store_empty", args=self.__data(**kwds)) + + @parseJson() + def size(self, **kwds): + return self._raw_execute("object_store_size", args=self.__data(**kwds)) + + @parseJson() + def delete(self, **kwds): + return self._raw_execute("object_store_delete", args=self.__data(**kwds)) + + @parseJson() + def get_data(self, **kwds): + return self._raw_execute("object_store_get_data", args=self.__data(**kwds)) + + @parseJson() + def get_filename(self, **kwds): + return self._raw_execute("object_store_get_filename", args=self.__data(**kwds)) + + @parseJson() + def update_from_file(self, **kwds): + return self._raw_execute("object_store_update_from_file", args=self.__data(**kwds)) + + @parseJson() + def get_store_usage_percent(self): + return self._raw_execute("object_store_get_store_usage_percent", args={}) + + def __data(self, **kwds): + return kwds + + def _raw_execute(self, command, args={}): + return self.lwr_interface.execute(command, args, data=None, input_path=None, output_path=None) diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -19,6 +19,7 @@ from galaxy.util import unicodify as text_type from .client import Client, InputCachingClient +from .client import ObjectStoreClient from .transport import get_transport from .util import TransferEventManager from .destination import url_to_destination_params @@ -74,6 +75,26 @@ return destination_params +class ObjectStoreClientManager(object): + + def __init__(self, **kwds): + if 'object_store' in kwds: + self.interface_class = LocalLwrInterface + self.interface_args = dict(object_store=kwds['object_store']) + else: + self.interface_class = HttpLwrInterface + transport_type = kwds.get('transport_type', None) + transport = get_transport(transport_type) + self.interface_args = dict(transport=transport) + self.extra_client_kwds = {} + + def get_client(self, client_params): + interface_class = self.interface_class + interface_args = dict(destination_params=client_params, **self.interface_args) + interface = interface_class(**interface_args) + return ObjectStoreClient(interface) + + class JobManagerInteface(object): """ Abstract base class describes how client communicates with remote job @@ -114,9 +135,10 @@ class LocalLwrInterface(object): - def __init__(self, destination_params, job_manager, file_cache): + def __init__(self, destination_params, job_manager=None, file_cache=None, object_store=None): self.job_manager = job_manager self.file_cache = file_cache + self.object_store = object_store def __app_args(self): ## Arguments that would be specified from LwrApp if running @@ -124,6 +146,7 @@ return { 'manager': self.job_manager, 'file_cache': self.file_cache, + 'object_store': self.object_store, 'ip': None } @@ -204,4 +227,4 @@ int_val = int(val) return int_val -__all__ = [ClientManager, HttpLwrInterface] +__all__ = [ClientManager, ObjectStoreClientManager, HttpLwrInterface] diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -29,6 +29,7 @@ from galaxy.util import asbool, is_multi_byte, nice_size, Params, restore_text, send_mail from galaxy.util.bunch import Bunch from galaxy.util.hash_util import new_secure_hash +from galaxy.util.directory_hash import directory_hash_id from galaxy.web.framework.helpers import to_unicode from galaxy.web.form_builder import (AddressField, CheckboxField, HistoryField, PasswordField, SelectField, TextArea, TextField, WorkflowField, @@ -4012,18 +4013,3 @@ self.repository_id = repository_id self.repository_path = repository_path self.version = version - -## ---- Utility methods ------------------------------------------------------- - -def directory_hash_id( id ): - s = str( id ) - l = len( s ) - # Shortcut -- ids 0-999 go under ../000/ - if l < 4: - return [ "000" ] - # Pad with zeros until a multiple of three - padded = ( ( 3 - len( s ) % 3 ) * "0" ) + s - # Drop the last three digits -- 1000 files per directory - padded = padded[:-3] - # Break into chunks of three - return [ padded[i*3:(i+1)*3] for i in range( len( padded ) // 3 ) ] diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -9,14 +9,19 @@ import shutil import logging import threading +from xml.etree import ElementTree -from galaxy import util +from galaxy.util import umask_fix_perms, force_symlink from galaxy.exceptions import ObjectInvalid, ObjectNotFound -from galaxy.jobs import Sleeper -from galaxy.model import directory_hash_id +from galaxy.util.sleeper import Sleeper +from galaxy.util.directory_hash import directory_hash_id from galaxy.util.odict import odict +try: + from sqlalchemy.orm import object_session +except ImportError: + object_session = None -from sqlalchemy.orm import object_session +NO_SESSION_ERROR_MESSAGE = "Attempted to 'create' object store entity in configuration with no database session present." log = logging.getLogger( __name__ ) @@ -202,7 +207,7 @@ self.extra_dirs['job_work'] = config.job_working_directory self.extra_dirs['temp'] = config.new_file_path #The new config_xml overrides universe settings. - if config_xml: + if config_xml is not None: for e in config_xml: if e.tag == 'files_dir': self.file_path = e.get('path') @@ -290,8 +295,8 @@ os.makedirs(dir) # Create the file if it does not exist if not dir_only: - open(path, 'w').close() - util.umask_fix_perms(path, self.config.umask, 0666) + open(path, 'w').close() # Should be rb? + umask_fix_perms(path, self.config.umask, 0666) def empty(self, obj, **kwargs): return os.path.getsize(self.get_filename(obj, **kwargs)) == 0 @@ -320,7 +325,7 @@ return False def get_data(self, obj, start=0, count=-1, **kwargs): - data_file = open(self.get_filename(obj, **kwargs), 'r') + data_file = open(self.get_filename(obj, **kwargs), 'r') # Should be rb? data_file.seek(start) content = data_file.read(count) data_file.close() @@ -345,7 +350,7 @@ if file_name and self.exists(obj, **kwargs): try: if preserve_symlinks and os.path.islink( file_name ): - util.force_symlink( os.readlink( file_name ), self.get_filename( obj, **kwargs ) ) + force_symlink( os.readlink( file_name ), self.get_filename( obj, **kwargs ) ) else: shutil.copy( file_name, self.get_filename( obj, **kwargs ) ) except IOError, ex: @@ -358,7 +363,7 @@ def get_store_usage_percent(self): st = os.statvfs(self.file_path) - return (float(st.f_blocks - st.f_bavail)/st.f_blocks) * 100 + return ( float( st.f_blocks - st.f_bavail ) / st.f_blocks ) * 100 class CachingObjectStore(ObjectStore): @@ -428,7 +433,7 @@ return store.__getattribute__(method)(obj, **kwargs) if default_is_exception: raise default( 'objectstore, __call_method failed: %s on %s, kwargs: %s' - %( method, str( obj ), str( kwargs ) ) ) + % ( method, str( obj ), str( kwargs ) ) ) else: return default @@ -442,7 +447,7 @@ def __init__(self, config, config_xml=None, fsmon=False): super(DistributedObjectStore, self).__init__(config, config_xml=config_xml) - if not config_xml: + if config_xml is None: self.distributed_config = config.distributed_object_store_config_file assert self.distributed_config is not None, "distributed object store ('object_store = distributed') " \ "requires a config file, please set one in " \ @@ -462,10 +467,9 @@ self.filesystem_monitor_thread.start() log.info("Filesystem space monitor started") - def __parse_distributed_config(self, config, config_xml = None): - if not config_xml: - tree = util.parse_xml(self.distributed_config) - root = tree.getroot() + def __parse_distributed_config(self, config, config_xml=None): + if config_xml is None: + root = ElementTree.parse(self.distributed_config).getroot() log.debug('Loading backends for distributed object store from %s' % self.distributed_config) else: root = config_xml.find('backends') @@ -512,7 +516,7 @@ if pct > maxpct: new_weighted_backend_ids = filter(lambda x: x != id, new_weighted_backend_ids) self.weighted_backend_ids = new_weighted_backend_ids - self.sleeper.sleep(120) # Test free space every 2 minutes + self.sleeper.sleep(120) # Test free space every 2 minutes def create(self, obj, **kwargs): """ @@ -524,9 +528,8 @@ obj.object_store_id = random.choice(self.weighted_backend_ids) except IndexError: raise ObjectInvalid( 'objectstore.create, could not generate obj.object_store_id: %s, kwargs: %s' - %( str( obj ), str( kwargs ) ) ) - object_session( obj ).add( obj ) - object_session( obj ).flush() + % ( str( obj ), str( kwargs ) ) ) + create_object_in_session( obj ) log.debug("Selected backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id)) else: log.debug("Using preferred backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id)) @@ -538,7 +541,7 @@ return self.backends[object_store_id].__getattribute__(method)(obj, **kwargs) if default_is_exception: raise default( 'objectstore, __call_method failed: %s on %s, kwargs: %s' - %( method, str( obj ), str( kwargs ) ) ) + % ( method, str( obj ), str( kwargs ) ) ) else: return default @@ -554,8 +557,7 @@ if store.exists(obj, **kwargs): log.warning('%s object with ID %s found in backend object store with ID %s' % (obj.__class__.__name__, obj.id, id)) obj.object_store_id = id - object_session( obj ).add( obj ) - object_session( obj ).flush() + create_object_in_session( obj ) return id return None @@ -594,15 +596,14 @@ Depending on the configuration setting, invoke the appropriate object store """ - if not config_xml and config.object_store_config_file: + if config_xml is None and config.object_store_config_file: # This is a top level invocation of build_object_store_from_config, and # we have an object_store_conf.xml -- read the .xml and build # accordingly - tree = util.parse_xml(config.object_store_config_file) - root = tree.getroot() + root = ElementTree.parse(config.object_store_config_file).getroot() store = root.get('type') config_xml = root - elif config_xml: + elif config_xml is not None: store = config_xml.get('type') else: store = config.object_store @@ -610,21 +611,25 @@ if store == 'disk': return DiskObjectStore(config=config, config_xml=config_xml) elif store == 's3': - from galaxy.objectstore.s3 import S3ObjectStore + from .s3 import S3ObjectStore return S3ObjectStore(config=config, config_xml=config_xml) elif store == 'swift': - from galaxy.objectstore.s3 import SwiftObjectStore + from .s3 import SwiftObjectStore return SwiftObjectStore(config=config, config_xml=config_xml) elif store == 'distributed': return DistributedObjectStore(config=config, fsmon=fsmon, config_xml=config_xml) elif store == 'hierarchical': return HierarchicalObjectStore(config=config, config_xml=config_xml) elif store == 'irods': - from galaxy.objectstore.rods import IRODSObjectStore + from .rods import IRODSObjectStore return IRODSObjectStore(config=config, config_xml=config_xml) + elif store == 'lwr': + from .lwr import LwrObjectStore + return LwrObjectStore(config=config, config_xml=config_xml) else: log.error("Unrecognized object store definition: {0}".format(store)) + def local_extra_dirs( func ): """ A decorator for non-local plugins to utilize local directories for their extra_dirs (job_working_directory and temp). """ @@ -638,6 +643,7 @@ raise Exception( "Could not call DiskObjectStore's %s method, does your Object Store plugin inherit from DiskObjectStore?" % func.__name__ ) return wraps + def convert_bytes(bytes): """ A helper function used for pretty printing disk usage """ if bytes is None: @@ -659,3 +665,12 @@ else: size = '%.2fb' % bytes return size + + +def create_object_in_session( obj ): + session = object_session( obj ) if object_session is not None else None + if session is not None: + object_session( obj ).add( obj ) + object_session( obj ).flush() + else: + raise Exception( NO_SESSION_ERROR_MESSAGE ) diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/objectstore/lwr.py --- /dev/null +++ b/lib/galaxy/objectstore/lwr.py @@ -0,0 +1,76 @@ +from __future__ import absolute_import # Need to import lwr_client absolutely. +from ..objectstore import ObjectStore +try: + from galaxy.jobs.runners.lwr_client.manager import ObjectStoreClientManager +except ImportError: + from lwr.lwr_client.manager import ObjectStoreClientManager + + +class LwrObjectStore(ObjectStore): + """ + Object store implementation that delegates to a remote LWR server. + + This may be more aspirational than practical for now, it would be good to + Galaxy to a point that a handler thread could be setup that doesn't attempt + to access the disk files returned by a (this) object store - just passing + them along to the LWR unmodified. That modification - along with this + implementation and LWR job destinations would then allow Galaxy to fully + manage jobs on remote servers with completely different mount points. + + This implementation should be considered beta and may be dropped from + Galaxy at some future point or significantly modified. + """ + + def __init__(self, config, config_xml): + self.lwr_client = self.__build_lwr_client(config_xml) + + def exists(self, obj, **kwds): + return self.lwr_client.exists(**self.__build_kwds(obj, **kwds)) + + def file_ready(self, obj, **kwds): + return self.lwr_client.file_ready(**self.__build_kwds(obj, **kwds)) + + def create(self, obj, **kwds): + return self.lwr_client.create(**self.__build_kwds(obj, **kwds)) + + def empty(self, obj, **kwds): + return self.lwr_client.empty(**self.__build_kwds(obj, **kwds)) + + def size(self, obj, **kwds): + return self.lwr_client.size(**self.__build_kwds(obj, **kwds)) + + def delete(self, obj, **kwds): + return self.lwr_client.delete(**self.__build_kwds(obj, **kwds)) + + # TODO: Optimize get_data. + def get_data(self, obj, **kwds): + return self.lwr_client.get_data(**self.__build_kwds(obj, **kwds)) + + def get_filename(self, obj, **kwds): + return self.lwr_client.get_filename(**self.__build_kwds(obj, **kwds)) + + def update_from_file(self, obj, **kwds): + return self.lwr_client.update_from_file(**self.__build_kwds(obj, **kwds)) + + def get_store_usage_percent(self): + return self.lwr_client.get_store_usage_percent() + + def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): + return None + + def __build_kwds(self, obj, **kwds): + kwds['object_id'] = obj.id + return kwds + pass + + def __build_lwr_client(self, config_xml): + url = config_xml.get("url") + private_token = config_xml.get("private_token", None) + transport = config_xml.get("transport", None) + manager_options = dict(transport=transport) + client_options = dict(url=url, private_token=private_token) + lwr_client = ObjectStoreClientManager(**manager_options).get_client(client_options) + return lwr_client + + def shutdown(self): + pass diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/objectstore/rods.py --- a/lib/galaxy/objectstore/rods.py +++ b/lib/galaxy/objectstore/rods.py @@ -12,12 +12,17 @@ from posixpath import basename as path_basename from posixpath import dirname as path_dirname -from galaxy.objectstore import DiskObjectStore, ObjectStore, local_extra_dirs from galaxy.exceptions import ObjectNotFound +from ..objectstore import DiskObjectStore, ObjectStore, local_extra_dirs -import galaxy.eggs -galaxy.eggs.require( 'PyRods' ) -import irods +try: + import galaxy.eggs + galaxy.eggs.require( 'PyRods' ) + import irods +except ImportError: + irods = None + +NO_PYRODS_ERROR_MESSAGE = "IRODS object store configured, but no PyRods dependency available. Please install and properly configure PyRods or modify object store configuration." log = logging.getLogger( __name__ ) @@ -27,6 +32,8 @@ Galaxy object store based on iRODS """ def __init__( self, config, file_path=None, extra_dirs=None ): + if irods is None: + raise Exception(NO_PYRODS_ERROR_MESSAGE) super( IRODSObjectStore, self ).__init__( config, file_path=file_path, extra_dirs=extra_dirs ) self.cache_path = config.object_store_cache_path self.default_resource = config.irods_default_resource or None @@ -146,7 +153,7 @@ doi = irods.dataObjInp_t() doi.objPath = rods_path doi.createMode = 0640 - doi.dataSize = 0 # 0 actually means "unknown", although literally 0 would be preferable + doi.dataSize = 0 # 0 actually means "unknown", although literally 0 would be preferable irods.addKeyVal( doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource ) status = irods.rcDataObjCreate( self.rods_conn, doi ) assert status >= 0, 'create(): rcDataObjCreate() failed: %s: %s: %s' % ( rods_path, status, irods.strerror( status ) ) @@ -237,7 +244,7 @@ incoming_path = os.path.join( os.path.dirname( cached_path ), "__incoming_%s" % os.path.basename( cached_path ) ) doi = irods.dataObjInp_t() doi.objPath = self.__get_rods_path( obj, **kwargs ) - doi.dataSize = 0 # TODO: does this affect performance? should we get size? + doi.dataSize = 0 # TODO: does this affect performance? should we get size? doi.numThreads = 0 # TODO: might want to VERIFY_CHKSUM_KW log.debug( 'get_filename(): caching %s to %s', doi.objPath, incoming_path ) @@ -296,6 +303,7 @@ def get_store_usage_percent(self): return 0.0 + # monkeypatch an strerror method into the irods module def _rods_strerror( errno ): """ @@ -309,7 +317,9 @@ irods.__rods_strerror_map[ v ] = name return irods.__rods_strerror_map.get( errno, 'GALAXY_NO_ERRNO_MAPPING_FOUND' ) -irods.strerror = _rods_strerror +if irods is not None: + irods.strerror = _rods_strerror + def rods_connect(): """ diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -10,21 +10,26 @@ import subprocess from datetime import datetime -from galaxy import util -from galaxy.jobs import Sleeper -from galaxy.model import directory_hash_id -from galaxy.objectstore import ObjectStore, convert_bytes +from galaxy.util import umask_fix_perms +from galaxy.util.sleeper import Sleeper +from galaxy.util.directory_hash import directory_hash_id +from ..objectstore import ObjectStore, convert_bytes from galaxy.exceptions import ObjectNotFound import multiprocessing -from galaxy.objectstore.s3_multipart_upload import multipart_upload -import boto -from boto.s3.key import Key -from boto.s3.connection import S3Connection -from boto.exception import S3ResponseError +from .s3_multipart_upload import multipart_upload +try: + import boto + from boto.s3.key import Key + from boto.s3.connection import S3Connection + from boto.exception import S3ResponseError +except ImportError: + boto = None + +NO_BOTO_ERROR_MESSAGE = "S3/Swift object store configured, but no boto dependency available. Please install and properly configure boto or modify object store configuration." log = logging.getLogger( __name__ ) -logging.getLogger('boto').setLevel(logging.INFO) # Otherwise boto is quite noisy +logging.getLogger('boto').setLevel(logging.INFO) # Otherwise boto is quite noisy class S3ObjectStore(ObjectStore): @@ -34,6 +39,8 @@ Galaxy and S3. """ def __init__(self, config, config_xml): + if boto is None: + raise Exception(NO_BOTO_ERROR_MESSAGE) super(S3ObjectStore, self).__init__(config, config_xml) self.config = config self.staging_path = self.config.file_path @@ -82,7 +89,7 @@ raise def __cache_monitor(self): - time.sleep(2) # Wait for things to load before starting the monitor + time.sleep(2) # Wait for things to load before starting the monitor while self.running: total_size = 0 # Is this going to be too expensive of an operation to be done frequently? @@ -110,7 +117,7 @@ # For now, delete enough to leave at least 10% of the total cache free delete_this_much = total_size - cache_limit self.__clean_cache(file_list, delete_this_much) - self.sleeper.sleep(30) # Test cache size every 30 seconds? + self.sleeper.sleep(30) # Test cache size every 30 seconds? def __clean_cache(self, file_list, delete_this_much): """ Keep deleting files from the file_list until the size of the deleted @@ -154,7 +161,7 @@ log.debug("Using cloud object store with bucket '%s'" % bucket.name) return bucket except S3ResponseError: - log.debug("Could not get bucket '%s', attempt %s/5" % (bucket_name, i+1)) + log.debug("Could not get bucket '%s', attempt %s/5" % (bucket_name, i + 1)) time.sleep(2) # All the attempts have been exhausted and connection was not established, # raise error @@ -163,13 +170,13 @@ def _fix_permissions(self, rel_path): """ Set permissions on rel_path""" for basedir, dirs, files in os.walk(rel_path): - util.umask_fix_perms(basedir, self.config.umask, 0777, self.config.gid) + umask_fix_perms(basedir, self.config.umask, 0777, self.config.gid) for f in files: path = os.path.join(basedir, f) # Ignore symlinks if os.path.islink(path): continue - util.umask_fix_perms( path, self.config.umask, 0666, self.config.gid ) + umask_fix_perms( path, self.config.umask, 0666, self.config.gid ) def _construct_path(self, obj, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, **kwargs): rel_path = os.path.join(*directory_hash_id(obj.id)) @@ -283,7 +290,7 @@ return True else: log.debug("Pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))) - self.transfer_progress = 0 # Reset transfer progress counter + self.transfer_progress = 0 # Reset transfer progress counter key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10) return True except S3ResponseError, ex: @@ -315,14 +322,14 @@ mb_size = os.path.getsize(source_file) / 1e6 #DBTODO Hack, refactor this logic. if mb_size < 60 or type(self) == SwiftObjectStore: - self.transfer_progress = 0 # Reset transfer progress counter + self.transfer_progress = 0 # Reset transfer progress counter key.set_contents_from_filename(source_file, reduced_redundancy=self.use_rr, cb=self._transfer_cb, num_cb=10) else: multipart_upload(self.bucket, key.name, source_file, mb_size, use_rr=self.use_rr) end_time = datetime.now() # print "+ Push ended at '%s'; %s bytes transfered in %ssec" % (end_time, os.path.getsize(source_file), end_time-start_time) - log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)" % (source_file, rel_path, os.path.getsize(source_file), end_time-start_time)) + log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)" % (source_file, rel_path, os.path.getsize(source_file), end_time - start_time)) return True else: log.error("Tried updating key '%s' from source file '%s', but source file does not exist." @@ -408,7 +415,7 @@ return bool(self.size(obj, **kwargs) > 0) else: raise ObjectNotFound( 'objectstore.empty, object does not exist: %s, kwargs: %s' - %( str( obj ), str( kwargs ) ) ) + % ( str( obj ), str( kwargs ) ) ) def size(self, obj, **kwargs): rel_path = self._construct_path(obj, **kwargs) @@ -484,7 +491,7 @@ return cache_path # Check if the file exists in persistent storage and, if it does, pull it into cache elif self.exists(obj, **kwargs): - if dir_only: # Directories do not get pulled into cache + if dir_only: # Directories do not get pulled into cache return cache_path else: if self._pull_into_cache(rel_path): @@ -494,7 +501,7 @@ # if dir_only: # return cache_path raise ObjectNotFound( 'objectstore.get_filename, no cache_path: %s, kwargs: %s' - %( str( obj ), str( kwargs ) ) ) + % ( str( obj ), str( kwargs ) ) ) # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path def update_from_file(self, obj, file_name=None, create=False, **kwargs): @@ -520,14 +527,14 @@ self._push_to_os(rel_path, source_file) else: raise ObjectNotFound( 'objectstore.update_from_file, object does not exist: %s, kwargs: %s' - %( str( obj ), str( kwargs ) ) ) + % ( str( obj ), str( kwargs ) ) ) def get_object_url(self, obj, **kwargs): if self.exists(obj, **kwargs): rel_path = self._construct_path(obj, **kwargs) try: key = Key(self.bucket, rel_path) - return key.generate_url(expires_in = 86400) # 24hrs + return key.generate_url(expires_in=86400) # 24hrs except S3ResponseError, ex: log.warning("Trouble generating URL for dataset '%s': %s" % (rel_path, ex)) return None @@ -552,4 +559,3 @@ port=self.port, calling_format=boto.s3.connection.OrdinaryCallingFormat(), path=self.conn_path) - diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/objectstore/s3_multipart_upload.py --- a/lib/galaxy/objectstore/s3_multipart_upload.py +++ b/lib/galaxy/objectstore/s3_multipart_upload.py @@ -4,10 +4,8 @@ This parallelizes the task over available cores using multiprocessing. Code mostly taken form CloudBioLinux. """ -from __future__ import with_statement import os -import sys import glob import subprocess import contextlib @@ -16,10 +14,17 @@ import multiprocessing from multiprocessing.pool import IMapIterator -from galaxy import eggs -eggs.require('boto') +try: + from galaxy import eggs + eggs.require('boto') +except ImportError: + pass -import boto +try: + import boto +except ImportError: + boto = None + def map_wrap(f): @functools.wraps(f) diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/util/directory_hash.py --- /dev/null +++ b/lib/galaxy/util/directory_hash.py @@ -0,0 +1,23 @@ + + +def directory_hash_id( id ): + """ + + >>> directory_hash_id( 100 ) + ['000'] + >>> directory_hash_id( "90000" ) + ['090'] + >>> directory_hash_id("777777777") + ['000', '777', '777'] + """ + s = str( id ) + l = len( s ) + # Shortcut -- ids 0-999 go under ../000/ + if l < 4: + return [ "000" ] + # Pad with zeros until a multiple of three + padded = ( ( 3 - len( s ) % 3 ) * "0" ) + s + # Drop the last three digits -- 1000 files per directory + padded = padded[:-3] + # Break into chunks of three + return [ padded[ i * 3 : (i + 1 ) * 3 ] for i in range( len( padded ) // 3 ) ] diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f lib/galaxy/util/sleeper.py --- /dev/null +++ b/lib/galaxy/util/sleeper.py @@ -0,0 +1,22 @@ +import threading + + +class Sleeper( object ): + """ + Provides a 'sleep' method that sleeps for a number of seconds *unless* + the notify method is called (from a different thread). + """ + def __init__( self ): + self.condition = threading.Condition() + + def sleep( self, seconds ): + # Should this be in a try/finally block? -John + self.condition.acquire() + self.condition.wait( seconds ) + self.condition.release() + + def wake( self ): + # Should this be in a try/finally block? -John + self.condition.acquire() + self.condition.notify() + self.condition.release() diff -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 -r a540510a3091ad7cfe3c4680c8bb04a20679e44f test/unit/test_objectstore.py --- /dev/null +++ b/test/unit/test_objectstore.py @@ -0,0 +1,210 @@ +import os +from shutil import rmtree +from string import Template +from tempfile import mkdtemp +try: + from galaxy import objectstore +except ImportError: + from lwr import objectstore +from contextlib import contextmanager + +DISK_TEST_CONFIG = """<?xml version="1.0"?> +<object_store type="disk"> + <files_dir path="${temp_directory}/files1"/> + <extra_dir type="temp" path="${temp_directory}/tmp1"/> + <extra_dir type="job_work" path="${temp_directory}/job_working_directory1"/> +</object_store> +""" + + +def test_disk_store(): + with TestConfig(DISK_TEST_CONFIG) as (directory, object_store): + # Test no dataset with id 1 exists. + absent_dataset = MockDataset(1) + assert not object_store.exists(absent_dataset) + + # Write empty dataset 2 in second backend, ensure it is empty and + # exists. + empty_dataset = MockDataset(2) + directory.write(b"", "files1/000/dataset_2.dat") + assert object_store.exists(empty_dataset) + assert object_store.empty(empty_dataset) + + # Write non-empty dataset in backend 1, test it is not emtpy & exists. + hello_world_dataset = MockDataset(3) + directory.write(b"Hello World!", "files1/000/dataset_3.dat") + assert object_store.exists(hello_world_dataset) + assert not object_store.empty(hello_world_dataset) + + # Test get_data + data = object_store.get_data(hello_world_dataset) + assert data == b"Hello World!" + + data = object_store.get_data(hello_world_dataset, start=1, count=6) + assert data == b"ello W" + + # Test Size + + # Test absent and empty datasets yield size of 0. + assert object_store.size(absent_dataset) == 0 + assert object_store.size(empty_dataset) == 0 + # Elsewise + assert object_store.size(hello_world_dataset) > 0 # Should this always be the number of bytes? + + # Test percent used (to some degree) + percent_store_used = object_store.get_store_usage_percent() + assert percent_store_used > 0.0 + assert percent_store_used < 100.0 + + # Test update_from_file test + output_dataset = MockDataset(4) + output_real_path = os.path.join(directory.temp_directory, "files1", "000", "dataset_4.dat") + assert not os.path.exists(output_real_path) + output_working_path = directory.write(b"NEW CONTENTS", "job_working_directory1/example_output") + object_store.update_from_file(output_dataset, file_name=output_working_path, create=True) + assert os.path.exists(output_real_path) + + # Test delete + to_delete_dataset = MockDataset(5) + to_delete_real_path = directory.write(b"content to be deleted!", "files1/000/dataset_5.dat") + assert object_store.exists(to_delete_dataset) + assert object_store.delete(to_delete_dataset) + assert not object_store.exists(to_delete_dataset) + assert not os.path.exists(to_delete_real_path) + + +HIERARCHICAL_TEST_CONFIG = """<?xml version="1.0"?> +<object_store type="hierarchical"> + <backends> + <backend id="files1" type="disk" weight="1" order="0"> + <files_dir path="${temp_directory}/files1"/> + <extra_dir type="temp" path="${temp_directory}/tmp1"/> + <extra_dir type="job_work" path="${temp_directory}/job_working_directory1"/> + </backend> + <backend id="files2" type="disk" weight="1" order="1"> + <files_dir path="${temp_directory}/files2"/> + <extra_dir type="temp" path="${temp_directory}/tmp2"/> + <extra_dir type="job_work" path="${temp_directory}/job_working_directory2"/> + </backend> + </backends> +</object_store> +""" + + +def test_hierarchical_store(): + with TestConfig(HIERARCHICAL_TEST_CONFIG) as (directory, object_store): + + # Test no dataset with id 1 exists. + assert not object_store.exists(MockDataset(1)) + + # Write empty dataset 2 in second backend, ensure it is empty and + # exists. + directory.write("", "files2/000/dataset_2.dat") + assert object_store.exists(MockDataset(2)) + assert object_store.empty(MockDataset(2)) + + # Write non-empty dataset in backend 1, test it is not emtpy & exists. + directory.write("Hello World!", "files1/000/dataset_3.dat") + assert object_store.exists(MockDataset(3)) + assert not object_store.empty(MockDataset(3)) + + # Assert creation always happens in first backend. + for i in range(100): + dataset = MockDataset(100 + i) + object_store.create(dataset) + assert object_store.get_filename(dataset).find("files1") > 0 + + +DISTRIBUTED_TEST_CONFIG = """<?xml version="1.0"?> +<object_store type="distributed"> + <backends> + <backend id="files1" type="disk" weight="2" order="0"> + <files_dir path="${temp_directory}/files1"/> + <extra_dir type="temp" path="${temp_directory}/tmp1"/> + <extra_dir type="job_work" path="${temp_directory}/job_working_directory1"/> + </backend> + <backend id="files2" type="disk" weight="1" order="1"> + <files_dir path="${temp_directory}/files2"/> + <extra_dir type="temp" path="${temp_directory}/tmp2"/> + <extra_dir type="job_work" path="${temp_directory}/job_working_directory2"/> + </backend> + </backends> +</object_store> +""" + + +def test_distributed_store(): + with TestConfig(DISTRIBUTED_TEST_CONFIG) as (directory, object_store): + with __stubbed_persistence() as persisted_ids: + for i in range(100): + dataset = MockDataset(100 + i) + object_store.create(dataset) + + ## Test distributes datasets between backends according to weights + backend_1_count = len([v for v in persisted_ids.values() if v == "files1"]) + backend_2_count = len([v for v in persisted_ids.values() if v == "files2"]) + + assert backend_1_count > 0 + assert backend_2_count > 0 + assert backend_1_count > backend_2_count + + +class TestConfig(object): + def __init__(self, config_xml): + self.temp_directory = mkdtemp() + self.write(config_xml, "store.xml") + config = MockConfig(self.temp_directory) + self.object_store = objectstore.build_object_store_from_config(config) + + def __enter__(self): + return self, self.object_store + + def __exit__(self, type, value, tb): + rmtree(self.temp_directory) + + def write(self, contents, name): + path = os.path.join(self.temp_directory, name) + directory = os.path.dirname(path) + if not os.path.exists(directory): + os.makedirs(directory) + expanded_contents = Template(contents).safe_substitute(temp_directory=self.temp_directory) + open(path, "w").write(expanded_contents) + return path + + +class MockConfig(object): + + def __init__(self, temp_directory): + self.file_path = temp_directory + self.object_store_config_file = os.path.join(temp_directory, "store.xml") + self.object_store_check_old_style = False + self.job_working_directory = temp_directory + self.new_file_path = temp_directory + self.umask = 0000 + + +class MockDataset(object): + + def __init__(self, id): + self.id = id + self.object_store_id = None + + +## Poor man's mocking. Need to get a real mocking library as real Galaxy development +## dependnecy. +PERSIST_METHOD_NAME = "create_object_in_session" + + +@contextmanager +def __stubbed_persistence(): + real_method = getattr(objectstore, PERSIST_METHOD_NAME) + try: + persisted_ids = {} + + def persist(object): + persisted_ids[object.id] = object.object_store_id + setattr(objectstore, PERSIST_METHOD_NAME, persist) + yield persisted_ids + + finally: + setattr(objectstore, PERSIST_METHOD_NAME, real_method) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Refactoring code cleanup for installing tool dependencies from the tool shed into Galaxy.
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3116103966fa/ Changeset: 3116103966fa User: greg Date: 2013-12-03 17:01:20 Summary: Refactoring code cleanup for installing tool dependencies from the tool shed into Galaxy. Affected #: 4 files diff -r dd53fe2a3e7308ccd7a007f78ae6e29b7eff9ef0 -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3631,6 +3631,11 @@ return False @property + def is_deactivated_or_installed( self ): + return self.status in [ self.installation_status.DEACTIVATED, + self.installation_status.INSTALLED ] + + @property def is_latest_installable_revision( self ): if self.tool_shed_status: return galaxy.util.asbool( self.tool_shed_status.get( 'latest_installable_revision', False ) ) diff -r dd53fe2a3e7308ccd7a007f78ae6e29b7eff9ef0 -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -37,11 +37,30 @@ def append_line( self, skip_if_contained=True, make_executable=True, **kwd ): env_var_dict = dict( **kwd ) - env_entry, env_file = td_common_util.create_or_update_env_shell_file( self.install_dir, env_var_dict ) + env_entry, env_file = self.create_or_update_env_shell_file( self.install_dir, env_var_dict ) return_code = file_append( env_entry, env_file, skip_if_contained=skip_if_contained, make_executable=make_executable ) self.return_code = self.return_code or return_code return self.return_code + def create_or_update_env_shell_file( self, install_dir, env_var_dict ): + env_var_action = env_var_dict[ 'action' ] + env_var_value = env_var_dict[ 'value' ] + if env_var_action in [ 'prepend_to', 'set_to', 'append_to' ]: + env_var_name = env_var_dict[ 'name' ] + if env_var_action == 'prepend_to': + changed_value = '%s:$%s' % ( env_var_value, env_var_name ) + elif env_var_action == 'set_to': + changed_value = '%s' % env_var_value + elif env_var_action == 'append_to': + changed_value = '$%s:%s' % ( env_var_name, env_var_value ) + line = "%s=%s; export %s" % ( env_var_name, changed_value, env_var_name ) + elif env_var_action == "source": + line = ". %s" % env_var_value + else: + raise Exception( "Unknown shell file action %s" % env_var_action ) + env_shell_file_path = os.path.join( install_dir, 'env.sh' ) + return line, env_shell_file_path + class InstallEnvironment( object ): """Object describing the environment built up as part of the process of building and installing a package.""" diff -r dd53fe2a3e7308ccd7a007f78ae6e29b7eff9ef0 -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -216,7 +216,7 @@ if can_install_tool_dependency: # Set this dependent repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package. # We can get everything we need from the discovered installed required_repository. - if required_repository.is_installed: + if required_repository.is_deactivated_or_installed: if not os.path.exists( required_repository_package_install_dir ): print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) repo_files_dir = required_repository.repo_files_directory( app ) @@ -848,20 +848,29 @@ type='set_environment', status=app.model.ToolDependency.installation_status.INSTALLING, set_status=True ) - env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) if env_var_version == '1.0': - # Handle setting environment variables using a fabric method. - fabric_util.file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) - sa_session.refresh( tool_dependency ) - if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, - app.model.ToolDependency.installation_status.INSTALLED ]: + # Create this tool dependency's env.sh file. + env_file_builder = fabric_util.EnvFileBuilder( install_dir ) + return_code = env_file_builder.append_line( skip_if_contained=True, make_executable=True, **env_var_dict ) + if return_code: + error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \ + ( str( tool_dependency.name ), str( return_code ) ) + log.debug( error_message ) tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLED, - error_message=None, + status=app.model.ToolDependency.installation_status.ERROR, + error_message=error_message, remove_from_disk=False ) - log.debug( 'Environment variable %s set in %s for tool dependency %s.' % \ - ( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) ) + else: + if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, + app.model.ToolDependency.installation_status.INSTALLED ]: + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLED, + error_message=None, + remove_from_disk=False ) + log.debug( 'Environment variable %s set in %s for tool dependency %s.' % \ + ( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) ) else: error_message = 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).' tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, diff -r dd53fe2a3e7308ccd7a007f78ae6e29b7eff9ef0 -r 3116103966fa1cd6c942aa918bcd647f39c0aae3 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -145,25 +145,6 @@ return dict( name=env_var_name, action=env_var_action, value=elem.text) return None -def create_or_update_env_shell_file( install_dir, env_var_dict ): - env_var_action = env_var_dict[ 'action' ] - env_var_value = env_var_dict[ 'value' ] - if env_var_action in ['prepend_to', 'set_to', 'append_to']: - env_var_name = env_var_dict[ 'name' ] - if env_var_action == 'prepend_to': - changed_value = '%s:$%s' % ( env_var_value, env_var_name ) - elif env_var_action == 'set_to': - changed_value = '%s' % env_var_value - elif env_var_action == 'append_to': - changed_value = '$%s:%s' % ( env_var_name, env_var_value ) - line = "%s=%s; export %s" % ( env_var_name, changed_value, env_var_name ) - elif env_var_action == "source": - line = ". %s" % env_var_value - else: - raise Exception( "Unknown shell file action %s" % env_var_action ) - env_shell_file_path = os.path.join( install_dir, 'env.sh' ) - return line, env_shell_file_path - def download_binary( url, work_dir ): ''' Download a pre-compiled binary from the specified URL. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix for determining if a required tool dependency is in an error state.
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dd53fe2a3e73/ Changeset: dd53fe2a3e73 User: greg Date: 2013-12-03 15:35:05 Summary: Fix for determining if a required tool dependency is in an error state. Affected #: 2 files diff -r a62c54ddbe2a845be9f0ee2dc4fe4b5820bcd70c -r dd53fe2a3e7308ccd7a007f78ae6e29b7eff9ef0 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3631,11 +3631,6 @@ return False @property - def is_installed( self ): - return self.status in [ self.installation_status.DEACTIVATED, - self.installation_status.INSTALLED ] - - @property def is_latest_installable_revision( self ): if self.tool_shed_status: return galaxy.util.asbool( self.tool_shed_status.get( 'latest_installable_revision', False ) ) diff -r a62c54ddbe2a845be9f0ee2dc4fe4b5820bcd70c -r dd53fe2a3e7308ccd7a007f78ae6e29b7eff9ef0 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -98,9 +98,9 @@ tool_dependency, error_message, remove_installation_path=False ) - elif required_tool_dependency.in_error_state: - error_message = "This tool dependency's required tool dependency %s has status %s." % \ - ( str( required_tool_dependency.name ), str( required_tool_dependency.status ) ) + elif required_tool_dependency is not None and required_tool_dependency.in_error_state: + error_message = "This tool dependency's required tool dependency %s version %s has status %s." % \ + ( str( required_tool_dependency.name ), str( required_tool_dependency.version ), str( required_tool_dependency.status ) ) tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, tool_dependency, error_message, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: UI: Improve masthead, simplify code
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a62c54ddbe2a/ Changeset: a62c54ddbe2a User: guerler Date: 2013-12-03 07:42:58 Summary: UI: Improve masthead, simplify code Affected #: 4 files diff -r f1729c6dcba86603a9e471688df633251511a22b -r a62c54ddbe2a845be9f0ee2dc4fe4b5820bcd70c static/scripts/galaxy.masthead.js --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -14,20 +14,11 @@ // options options : null, - // item list - list : {}, - - // keeps track of the last element - itemLast: null, - - // counter - itemCounter: 0, - // background $background: null, - // flag indicating visibility of background - backgroundVisible: false, + // list + list: [], // initialize initialize : function(options) @@ -47,9 +38,7 @@ // assign background this.$background = $(this.el).find('#masthead-background'); - // loop through item specific unload functions - // and collect all there warning messages, regarding - // the user's attempt to unload the page + // loop through unload functions if the user attempts to unload the page var self = this; window.onbeforeunload = function() { @@ -68,7 +57,7 @@ // configure events events: { - 'click' : '_eventRefresh', + 'click' : '_click', 'mousedown' : function(e) { e.preventDefault() } }, @@ -84,32 +73,36 @@ return this._add(item, false); }, + // activate + highlight: function(id) + { + var current = $(this.el).find('#' + id + '> li'); + if (current) { + current.addClass('active'); + } + }, + // adds a new item to the masthead _add : function(item, append) { - var $loc = $(this.el).find('#' + item.mastheadLocation); + var $loc = $(this.el).find('#' + item.location); if ($loc) { // create frame for new item - var itemId = 'masthead-item-' + this.itemCounter++; - var $itemNew = $(item.el); + var $current = $(item.el); - // configure id and class in order to mark new items - $itemNew.attr('id', itemId); - $itemNew.addClass('masthead-item'); + // configure class in order to mark new items + $current.addClass('masthead-item'); // append to masthead if (append) { - $loc.append($itemNew); + $loc.append($current); } else { - $loc.prepend($itemNew); + $loc.prepend($current); } // add to list - this.list[itemId] = item; - - // return item id - return itemId; + this.list.push(item); } // location not found @@ -117,63 +110,27 @@ }, // handle click event - _eventRefresh: function(e) + _click: function(e) { - // identify current item - var itemCurrent = $(e.target).closest('.masthead-item'); - - // get identifier - if (itemCurrent.length) - itemCurrent = itemCurrent.attr('id'); - - // check last item - if (this.itemLast && this.itemLast != itemCurrent) - { - var it = this.list[this.itemLast]; - if (it) { - if (it.mastheadReset) { - it.mastheadReset(); - } - } + // close all popups + var $all = $(this.el).find('.popup'); + if ($all) { + $all.hide(); } - // check if current item is in active state - var useBackground = false; - if (itemCurrent) - { - var it = this.list[itemCurrent]; - if (it) { - if (it.mastheadReset) { - if (this.itemLast == itemCurrent) { - useBackground = this.backgroundVisible ? false : true; - } else { - useBackground = true; - } - } - } - } - - // decide wether to show/hide background - if (useBackground) { + // open current item + var $current = $(e.target).closest('.masthead-item').find('.popup'); + if ($(e.target).hasClass('head')) { + $current.show(); this.$background.show(); } else { this.$background.hide(); } - - // backup - this.backgroundVisible = useBackground; - this.itemLast = itemCurrent; }, /* HTML TEMPLATES */ - - // template item - _templateItem: function(id) - { - return '<div id="' + id + '" class="masthead-item"></div>'; - }, // fill template _template: function(options) @@ -202,9 +159,9 @@ // icon options options: { - id : "galaxy-icon", - icon : "fa-cog", - tooltip : "galaxy-icon", + id : '', + icon : 'fa-cog', + tooltip : '', with_number : false, on_click : function() { alert ('clicked') }, on_unload : null, @@ -212,7 +169,7 @@ }, // location identifier for masthead class - mastheadLocation: 'iconbar', + location: 'iconbar', // initialize initialize: function (options) @@ -278,7 +235,7 @@ // fill template icon _template: function (options) { - var tmpl = '<div id=' + options.id + ' class="symbol">' + + var tmpl = '<div id="' + options.id + '" class="symbol">' + '<div class="icon fa fa-2x ' + options.icon + '"></div>'; if (options.with_number) tmpl+= '<div class="number"></div>'; @@ -296,7 +253,7 @@ options: { id : '', - title : 'Title', + title : '', target : '_parent', content : '', type : 'url', @@ -306,18 +263,15 @@ }, // location - mastheadLocation: 'navbar', + location: 'navbar', // optional sub menu $menu: null, - // flag if menu is visible - menuVisible: false, - // events events: { - 'click .head' : '_eventClickHead' + 'click .head' : '_head' }, // initialize @@ -352,7 +306,7 @@ }, // add menu item - addMenu: function (options) + add: function (options) { // menu option defaults var menuOptions = { @@ -382,7 +336,7 @@ $(this.el).find('.symbol').addClass('caret'); // update element link - this.$menu = $(this.el).find('.menu'); + this.$menu = $(this.el).find('.popup'); } // create @@ -397,9 +351,6 @@ { // prevent default e.preventDefault(); - - // check for menu options - self._hideMenu(); // no modifications if new tab is requested if (self.options.target === '_blank') @@ -414,42 +365,14 @@ this.$menu.append($(this._templateDivider())); }, - // add reset function called by masthead - mastheadReset: function() - { - this._hideMenu(); - }, - - // hide menu - _hideMenu: function() - { - if (this.$menu && this.menuVisible) - { - this.$menu.hide(); - this.menuVisible = false; - } - }, - // show menu on header click - _eventClickHead: function(e) + _head: function(e) { // prevent default e.preventDefault(); // check for menu options - if (this.$menu) - { - // show/hide menu - if (!this.menuVisible) - { - this.$menu.show(); - this.menuVisible = true; - } else { - this.$menu.hide(); - this.menuVisible = false; - } - } else { - // open new frame + if (!this.$menu) { Galaxy.frame.add(this.options); } }, @@ -463,7 +386,7 @@ // fill template header _templateMenu: function () { - return '<ul class="menu dropdown-menu"></ul>'; + return '<ul class="popup dropdown-menu"></ul>'; }, _templateDivider: function() @@ -475,7 +398,7 @@ _template: function (options) { // start template - var tmpl = '<ul class="nav navbar-nav" border="0" cellspacing="0">' + + var tmpl = '<ul id="' + options.id + '" class="nav navbar-nav" border="0" cellspacing="0">' + '<li class="root dropdown" style="">' + '<a class="head dropdown-toggle" data-toggle="dropdown" target="' + options.target + '" href="' + options.content + '">' + options.title + '<b class="symbol"></b>' + diff -r f1729c6dcba86603a9e471688df633251511a22b -r a62c54ddbe2a845be9f0ee2dc4fe4b5820bcd70c static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -29,6 +29,7 @@ // Analyze data tab. // var tab_analysis = new mod_masthead.GalaxyMastheadTab({ + id : "analysis", title : "Analyze Data", content : "root/index" }); @@ -38,6 +39,7 @@ // Workflow tab. // var tab_workflow = new mod_masthead.GalaxyMastheadTab({ + id : "workflow", title : "Workflow", content : "workflow" @@ -48,33 +50,34 @@ // 'Shared Items' or Libraries tab. // var tab_shared = new mod_masthead.GalaxyMastheadTab({ + id : "shared", title : "Shared Data", content : "library/index" }); - tab_shared.addMenu({ + tab_shared.add({ title : "Data Libraries", content : "library/index", divider : true }); - tab_shared.addMenu({ + tab_shared.add({ title : "Published Histories", content : "history/list_published" }); - tab_shared.addMenu({ + tab_shared.add({ title : "Published Workflows", content : "workflow/list_published" }); - tab_shared.addMenu({ + tab_shared.add({ title : "Published Visualizations", content : "visualization/list_published" }); - tab_shared.addMenu({ + tab_shared.add({ title : "Published Pages", content : "page/list_published" }); @@ -87,17 +90,18 @@ if (this.options.user.requests) { var tab_lab = new mod_masthead.GalaxyMastheadTab({ + id : "lab", title : "Lab" }); - tab_lab.addMenu({ + tab_lab.add({ title : "Sequencing Requests", content : "requests/index" }); - tab_lab.addMenu({ + tab_lab.add({ title : "Find Samples", content : "requests/find_samples_index" }); - tab_lab.addMenu({ + tab_lab.add({ title : "Help", content : this.options.lims_doc_url }); @@ -108,16 +112,16 @@ // Visualization tab. // var tab_visualization = new mod_masthead.GalaxyMastheadTab({ - + id : "visualization", title : "Visualization", content : "visualization/list" }); - tab_visualization.addMenu({ + tab_visualization.add({ title : "New Track Browser", content : "visualization/trackster", target : "_frame" }); - tab_visualization.addMenu({ + tab_visualization.add({ title : "Saved Visualizations", content : "visualization/list", target : "_frame" @@ -130,10 +134,11 @@ if (this.options.enable_cloud_launch) { var tab_cloud = new mod_masthead.GalaxyMastheadTab({ + id : "cloud", title : "Cloud", content : "cloudlaunch/index" }); - tab_cloud.addMenu({ + tab_cloud.add({ title : "New Cloud Cluster", content : "cloudlaunch/index" }); @@ -146,6 +151,7 @@ if (this.options.is_admin_user) { var tab_admin = new mod_masthead.GalaxyMastheadTab({ + id : "admin", title : "Admin", content : "admin/index", extra_class : "admin-only" @@ -157,54 +163,55 @@ // Help tab. // var tab_help = new mod_masthead.GalaxyMastheadTab({ + id : "help", title : "Help" }); if (this.options.biostar_url) { - tab_help.addMenu({ + tab_help.add({ title : "Galaxy Q&A Site", content : this.options.biostar_url_redirect, target : "_blank" }); - tab_help.addMenu({ + tab_help.add({ title : "Ask a question", content : "biostar/biostar_question_redirect", target : "_blank" }); } - tab_help.addMenu({ + tab_help.add({ title : "Support", content : this.options.support_url, target : "_blank" }); - tab_help.addMenu({ + tab_help.add({ title : "Search", content : this.options.search_url, target : "_blank" }); - tab_help.addMenu({ + tab_help.add({ title : "Mailing Lists", content : this.options.mailing_lists, target : "_blank" }); - tab_help.addMenu({ + tab_help.add({ title : "Videos", content : this.options.screencasts_url, target : "_blank" }); - tab_help.addMenu({ + tab_help.add({ title : "Wiki", content : this.options.wiki_url, target : "_blank" }); - tab_help.addMenu({ + tab_help.add({ title : "How to Cite Galaxy", content : this.options.citation_url, target : "_blank" }); if (!this.options.terms_url) { - tab_help.addMenu({ + tab_help.add({ title : "Terms and Conditions", content : this.options.terms_url, target : "_blank" @@ -218,12 +225,13 @@ if (!this.options.user.valid) { var tab_user = new mod_masthead.GalaxyMastheadTab({ + id : "user", title : "User", extra_class : "loggedout-only" }); // login - tab_user.addMenu({ + tab_user.add({ title : "Login", content : "user/login", target : "galaxy_main" @@ -232,7 +240,7 @@ // register if (this.options.allow_user_creation) { - tab_user.addMenu({ + tab_user.add({ title : "Register", content : "user/create", target : "galaxy_main" @@ -243,37 +251,38 @@ this.masthead.append(tab_user); } else { var tab_user = new mod_masthead.GalaxyMastheadTab({ + id : "user", title : "User", extra_class : "loggedin-only" }); // show user logged in info - tab_user.addMenu({ + tab_user.add({ title : "Logged in as " + this.options.user.email }); // remote user if (this.options.use_remote_user && this.options.remote_user_logout_href) { - tab_user.addMenu({ + tab_user.add({ title : "Logout", content : this.options.remote_user_logout_href, target : "_top" }); } else { - tab_user.addMenu({ + tab_user.add({ title : "Preferences", content : "user?cntrller=user", target : "galaxy_main" }); - tab_user.addMenu({ + tab_user.add({ title : "Custom Builds", content : "user/dbkeys", target : "galaxy_main" }); - tab_user.addMenu({ + tab_user.add({ title : "Logout", content : "user/logout", target : "_top", @@ -282,23 +291,23 @@ } // default tabs - tab_user.addMenu({ + tab_user.add({ title : "Saved Histories", content : "history/list", target : "galaxy_main" }); - tab_user.addMenu({ + tab_user.add({ title : "Saved Datasets", content : "dataset/list", target : "galaxy_main" }); - tab_user.addMenu({ + tab_user.add({ title : "Saved Pages", content : "page/list", target : "_top" }); - tab_user.addMenu({ + tab_user.add({ title : "API Keys", content : "user/api_keys?cntrller=user", target : "galaxy_main" @@ -306,7 +315,7 @@ if (this.options.use_remote_user) { - tab_user.addMenu({ + tab_user.add({ title : "Public Name", content : "user/edit_username?cntrller=user", target : "galaxy_main" @@ -316,6 +325,10 @@ // add to masthead this.masthead.append(tab_user); } + + // identify active tab + if (this.options.active_view) + this.masthead.highlight(this.options.active_view); } }); diff -r f1729c6dcba86603a9e471688df633251511a22b -r a62c54ddbe2a845be9f0ee2dc4fe4b5820bcd70c templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -14,5 +14,7 @@ ## Masthead <%def name="masthead()"> - <% mod_masthead.load(); %> + <% + mod_masthead.load(self.active_view); + %></%def> \ No newline at end of file diff -r f1729c6dcba86603a9e471688df633251511a22b -r a62c54ddbe2a845be9f0ee2dc4fe4b5820bcd70c templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -28,7 +28,7 @@ </%def> ## masthead head generator -<%def name="load()"> +<%def name="load(active_view = None)"><% ## get configuration masthead_config = { @@ -51,7 +51,8 @@ 'allow_user_creation' : app.config.allow_user_creation, 'logo_url' : h.url_for(app.config.get( 'logo_url', '/')), 'is_admin_user' : trans.user and app.config.is_admin_user(trans.user), - + 'active_view' : active_view, + ## user details 'user' : { 'requests' : bool(trans.user and (trans.user.requests or trans.app.security_agent.get_accessible_request_types(trans, trans.user))), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix type in my last commit - thanks John!
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f1729c6dcba8/ Changeset: f1729c6dcba8 User: greg Date: 2013-12-03 03:35:00 Summary: Fix type in my last commit - thanks John! Affected #: 1 file diff -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece -r f1729c6dcba86603a9e471688df633251511a22b lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1533,7 +1533,7 @@ if file_name: if os.path.exists( file_name ): try: - os.remove( dir ) + os.remove( file_name ) except: pass Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Tweak changeset 5b8c91e4183664c90f4d95699ab971e674ffd67d which created symlinks to a required tool dep endncy env.sh file for dependent tool dependencies being installed. This approach was better than the previous approach which parsed the requried repository's tool_dependencies.xml file to create the env.sh file. This changeset uses a slightly different approach: it creates an env.sh file for the dependent tool dependency whose first line "sources" the required
by commits-noreply＠bitbucket.org 03 Dec '13

03 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cac7a527140e/ Changeset: cac7a527140e User: greg Date: 2013-12-03 02:36:59 Summary: Tweak changeset 5b8c91e4183664c90f4d95699ab971e674ffd67d which created symlinks to a required tool dep endncy env.sh file for dependent tool dependencies being installed. This approach was better than the previous approach which parsed the requried repository's tool_dependencies.xml file to create the env.sh file. This changeset uses a slightly different approach: it creates an env.sh file for the dependent tool dependency whose first line "sources" the required tool dende pendcy's env.sh file. This allows for the dependent env.sh file to be managed by its tool dependency (e.g., its tool dependency may require additional env.sh paths beyond those contained in the requyired tool dependency's env.sh file). This changeset also handles sysncing the database with the file system when tool dependencies are being installed when handling a complex repository dependency definition. This process used to be handled only when not dealing with a complex repository dependency definition. This fix should correct problems encounted by the Tool Shed's install and test framework which were introduced in 5b8c91e4183664c90f4d95699ab971e674ffd67d. Affected #: 5 files diff -r ef33472f0aa296e55fd811357e09366f9cee5467 -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3471,46 +3471,6 @@ def can_reinstall_or_activate( self ): return self.deleted - @property - def installing( self ): - """ - Used to determine if tool dependencies can denote this repository as - installing. - """ - return self.status not in [ self.installation_status.DEACTIVATED, - self.installation_status.UNINSTALLED, - self.installation_status.ERROR, - self.installation_status.INSTALLED, - self.installation_status.NEW, - ] - - @property - def installation_complete( self ): - """ - Used to determine if tool dependency installations can proceed. - Installed artifacts must be available on disk. - """ - return self.status in [ self.installation_status.DEACTIVATED, - self.installation_status.INSTALLED, - ] - - def to_dict( self, view='collection', value_mapper=None ): - if value_mapper is None: - value_mapper = {} - rval = {} - try: - visible_keys = self.__getattribute__( 'dict_' + view + '_visible_keys' ) - except AttributeError: - raise Exception( 'Unknown API view: %s' % view ) - for key in visible_keys: - try: - rval[ key ] = self.__getattribute__( key ) - if key in value_mapper: - rval[ key ] = value_mapper.get( key, rval[ key ] ) - except AttributeError: - rval[ key ] = None - return rval - def get_shed_config_filename( self ): shed_config_filename = None if self.metadata: @@ -3659,7 +3619,8 @@ """Return the repository's tool dependencies that are currently installed.""" installed_dependencies = [] for tool_dependency in self.tool_dependencies: - if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED, ToolDependency.installation_status.ERROR ]: + if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED, + ToolDependency.installation_status.ERROR ]: installed_dependencies.append( tool_dependency ) return installed_dependencies @@ -3670,6 +3631,11 @@ return False @property + def is_installed( self ): + return self.status in [ self.installation_status.DEACTIVATED, + self.installation_status.INSTALLED ] + + @property def is_latest_installable_revision( self ): if self.tool_shed_status: return galaxy.util.asbool( self.tool_shed_status.get( 'latest_installable_revision', False ) ) @@ -3804,6 +3770,23 @@ shed_config_filename = property( get_shed_config_filename, set_shed_config_filename ) + def to_dict( self, view='collection', value_mapper=None ): + if value_mapper is None: + value_mapper = {} + rval = {} + try: + visible_keys = self.__getattribute__( 'dict_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[ key ] = self.__getattribute__( key ) + if key in value_mapper: + rval[ key ] = value_mapper.get( key, rval[ key ] ) + except AttributeError: + rval[ key ] = None + return rval + @property def tool_dependencies_being_installed( self ): dependencies_being_installed = [] diff -r ef33472f0aa296e55fd811357e09366f9cee5467 -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -40,14 +40,22 @@ raise Exception( message ) return None - -def find_complex_dependency_package( app, dependent_install_dir, required_install_dir, tool_shed_repository, required_repository, package_name, package_version, tool_dependencies_config ): +def create_tool_dependency_with_initialized_env_sh_file( app, dependent_install_dir, tool_shed_repository, required_repository, package_name, + package_version, tool_dependencies_config ): """ + Create or get a tool_dependency record that is defined by the received package_name and package_version. An env.sh file will be + created for the tool_dependency in the received dependent_install_dir. """ + #The received required_repository refers to a tool_shed_repository record that is defined as a complex repository dependency for this + # tool_dependency. The required_repository may or may not be currently installed (it doesn't matter). If it is installed, it is + # associated with a tool_dependency that has an env.sh file that this new tool_dependency must be able to locate and "source". If it + # is not installed, we can still determine where that env.sh file will be, so we'll initialize this new tool_dependency's env.sh file + # in either case. If the require repository end up with an installation error, this new tool dependency will still be fine because its + # containing repository will be defined as missing dependencies. tool_dependencies = [] if not os.path.exists( dependent_install_dir ): os.makedirs( dependent_install_dir ) - env_file = None + required_tool_dependency_env_file_path = None if tool_dependencies_config: required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config ) if required_td_tree: @@ -58,51 +66,52 @@ # <package name="bwa" version="0.5.9"> required_td_package_name = required_td_elem.get( 'name', None ) required_td_package_version = required_td_elem.get( 'version', None ) + # Check the database to see if we have a record for the required tool dependency (we may not which is ok). If we + # find a record, we need to see if it is in an error state and if so handle it appropriately. + required_tool_dependency = \ + tool_dependency_util.get_tool_dependency_by_name_version_type_repository( app, + required_repository, + required_td_package_name, + required_td_package_version, + 'package' ) if required_td_package_name == package_name and required_td_package_version == package_version: - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=package_name, - version=package_version, - type='package', - status=app.model.ToolDependency.installation_status.NEVER_INSTALLED, - set_status=True ) - - if required_repository.installing: - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLING ) - # What happens if dependent repository fails or is - # uninstalled during this process. - env_file = required_repository_package_env( app, package_name, package_version, required_repository ) - if required_repository.installation_complete: - if not os.path.exists( env_file ): - error_message = 'env.sh file %s for package %s in dependendent repository could not be found. Required repository has status %s.' % ( package_name, env_file, required_repository.status ) - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + # Get or create a database tool_dependency record with which the installed package on disk will be associated. + tool_dependency = \ + tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=package_name, + version=package_version, + type='package', + status=app.model.ToolDependency.installation_status.NEVER_INSTALLED, + set_status=True ) + # Create an env.sh file for the tool_dependency whose first line will source the env.sh file located in + # the path defined by required_tool_dependency_env_file_path. It doesn't matter if the required env.sh + # file currently exists.. + required_tool_dependency_env_file_path = \ + tool_dependency_util.get_required_repository_package_env_sh_path( app, package_name, package_version, required_repository ) + env_file_builder = fabric_util.EnvFileBuilder( tool_dependency.installation_directory( app ) ) + env_file_builder.append_line( action="source", value=required_tool_dependency_env_file_path ) + return_code = env_file_builder.return_code + if return_code: + error_message = 'Error defining env.sh file for package %s, return_code: %s' % ( str( package_name, str( return_code ) ) ) + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, tool_dependency, error_message, remove_installation_path=False ) - else: - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLED ) + elif required_tool_dependency.in_error_state: + error_message = "This tool dependency's required tool dependency %s has status %s." % \ + ( str( required_tool_dependency.name ), str( required_tool_dependency.status ) ) + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency, + error_message, + remove_installation_path=False ) else: - # Ekk - handling tool depednencies for a dependent - # repository that is not installed. - # - # Go ahead a return the env.sh file - Galaxy will - # proceed to create an invalid symbolic link. - # This is subtle-ly different than the previous - # behavior which would have recreated an env.sh - # from the the required repository's - # tool_dependencies.xml but since it was not - # installed all of the values inside would be - # invalid path modifications. Either way, this file - # is junk until the required repository is - # installed properly. - pass + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLED ) tool_dependencies.append( tool_dependency ) - return tool_dependencies, env_file - + return tool_dependencies def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ): """Return the absolute path to a specified disk file contained in a repository.""" @@ -157,6 +166,12 @@ def handle_complex_repository_dependency_for_package( app, elem, package_name, package_version, tool_shed_repository ): + """ + Inspect the repository defined by a complex repository dependency definition and take certain steps to enable installation + of the received package name and version to proceed. The received elem is the <repository> tag set which defines the complex + repository dependency. The received tool_shed_repository is the installed tool shed repository for which the tool dependency + defined by the received package_name and package_version is being installed. + """ handled_tool_dependencies = [] tool_shed = elem.attrib[ 'toolshed' ] required_repository_name = elem.attrib[ 'name' ] @@ -179,7 +194,7 @@ tool_dependency_type='package', tool_dependency_name=package_name, tool_dependency_version=package_version ) - # Define the this dependent repository's tool dependency installation directory that will contain the env.sh file with a path to the + # Define this dependent repository's tool dependency installation directory that will contain the env.sh file with a path to the # required repository's installed tool dependency package. dependent_install_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, repository_name=tool_shed_repository.name, @@ -188,58 +203,58 @@ tool_dependency_type='package', tool_dependency_name=package_name, tool_dependency_version=package_version ) - # Set this dependent repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package. - # We can get everything we need from the discovered installed required_repository. - if required_repository.installation_complete: - if not os.path.exists( required_repository_package_install_dir ): - print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) - repo_files_dir = required_repository.repo_files_directory( app ) - tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' ) - if tool_dependencies_config: - config_to_use = tool_dependencies_config + if os.path.exists( dependent_install_dir ): + # Notice that we'll throw away the following tool_dependency if it can be installed. + tool_dependency, can_install_tool_dependency = tool_dependency_util.sync_database_with_file_system( app, + tool_shed_repository, + package_name, + package_version, + dependent_install_dir, + tool_dependency_type='package' ) + else: + can_install_tool_dependency = True + if can_install_tool_dependency: + # Set this dependent repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package. + # We can get everything we need from the discovered installed required_repository. + if required_repository.is_installed: + if not os.path.exists( required_repository_package_install_dir ): + print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) + repo_files_dir = required_repository.repo_files_directory( app ) + tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' ) + if tool_dependencies_config: + config_to_use = tool_dependencies_config + else: + message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \ + ( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) ) + raise Exception( message ) else: - message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \ - ( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) ) - raise Exception( message ) + # Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision + # should be updated if it's not current. + text = get_updated_changeset_revisions_from_tool_shed( app=app, + tool_shed_url=tool_shed, + name=required_repository_name, + owner=required_repository_owner, + changeset_revision=required_repository_changeset_revision ) + if text: + updated_changeset_revisions = listify( text ) + # The list of changeset revisions is in reverse order, so the newest will be first. + required_repository_changeset_revision = updated_changeset_revisions[ 0 ] + # Make a call to the tool shed to get the required repository's tool_dependencies.xml file. + tmp_filename = create_temporary_tool_dependencies_config( app, + tool_shed, + required_repository_name, + required_repository_owner, + required_repository_changeset_revision ) + config_to_use = tmp_filename + handled_tool_dependencies = create_tool_dependency_with_initialized_env_sh_file( app=app, + dependent_install_dir=dependent_install_dir, + tool_shed_repository=tool_shed_repository, + required_repository=required_repository, + package_name=package_name, + package_version=package_version, + tool_dependencies_config=config_to_use ) + suc.remove_file( tmp_filename ) else: - # Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision - # should be updated if it's not current. - text = get_updated_changeset_revisions_from_tool_shed( app=app, - tool_shed_url=tool_shed, - name=required_repository_name, - owner=required_repository_owner, - changeset_revision=required_repository_changeset_revision ) - if text: - updated_changeset_revisions = listify( text ) - # The list of changeset revisions is in reverse order, so the newest will be first. - required_repository_changeset_revision = updated_changeset_revisions[ 0 ] - # Make a call to the tool shed to get the required repository's tool_dependencies.xml file. - tmp_filename = create_temporary_tool_dependencies_config( app, - tool_shed, - required_repository_name, - required_repository_owner, - required_repository_changeset_revision ) - config_to_use = tmp_filename - - tool_dependencies, package_env_sh_file = find_complex_dependency_package( - app=app, - dependent_install_dir=dependent_install_dir, - required_install_dir=required_repository_package_install_dir, - tool_shed_repository=tool_shed_repository, - required_repository=required_repository, - package_name=package_name, - package_version=package_version, - tool_dependencies_config=config_to_use - ) - if package_env_sh_file: - os.symlink( package_env_sh_file, os.path.join( dependent_install_dir, "env.sh" ) ) - if tmp_filename: - try: - os.remove( tmp_filename ) - except: - pass - for tool_dependency in tool_dependencies: - tool_dependency = __mark_tool_dependency_installed( app, tool_dependency) handled_tool_dependencies.append( tool_dependency ) else: message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ @@ -247,7 +262,6 @@ raise Exception( message ) return handled_tool_dependencies - def install_and_build_package_via_fabric( app, tool_dependency, actions_dict ): sa_session = app.model.context.current try: @@ -262,10 +276,9 @@ tool_dependency, error_message, remove_installation_path=False ) - tool_dependency = __mark_tool_dependency_installed( app, tool_dependency) + tool_dependency = tool_dependency_util.mark_tool_dependency_installed( app, tool_dependency ) return tool_dependency - def install_package( app, elem, tool_shed_repository, tool_dependencies=None ): # The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository. sa_session = app.model.context.current @@ -298,57 +311,14 @@ tool_dependency_version=package_version ) can_install_tool_dependency = True if os.path.exists( install_dir ): - # The tool dependency installation directory exists, check for the presence of fabric_util.INSTALLATION_LOG, - # which indicates a successful installation. This currently assumes that the tool dependency record will - # always exist in the database. - tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type_repository( app, - tool_shed_repository, - package_name, - package_version, - 'package' ) - if tool_dependency.status == app.model.ToolDependency.installation_status.INSTALLING: - # The tool dependency is in an Installing state, so we don't want to do anything to it. If the tool - # dependency is being installed by someone else, we don't want to interfere with that. This assumes - # the installation by "someone else" is not hung in an Installing state, which is a weakness if that - # "someone else" never repaired it. - log.debug( 'Skipping installation of tool dependency %s version %s because it has a status of %s' % \ - ( str( tool_dependency.name ), str( tool_dependency.version ), str( tool_dependency.status ) ) ) - can_install_tool_dependency = False - else: - tool_dependency_installation_directory_contents = os.listdir( install_dir ) - if fabric_util.INSTALLATION_LOG in tool_dependency_installation_directory_contents: - # Since this tool dependency's installation directory contains an installation log, we consider it to be - # installed. In some cases the record may be missing from the database due to some activity outside of - # the control of the Tool Shed. Since a new record was created for it and we don't know the state of the - # files on disk, we will set it to an error state (unless we are running Tool Shed functional tests - see - # below). - log.debug( 'Skipping installation of tool dependency %s version %s because it is installed in %s' % \ - ( str( tool_dependency.name ), str( tool_dependency.version ), str( install_dir ) ) ) - can_install_tool_dependency = False - if app.config.running_functional_tests: - # If we are running functional tests, the state will be set to Installed because previously compiled - # tool dependencies are not deleted by default, from the "install and test" framework.. - tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED - else: - error_message = 'The installation directory for this tool dependency had contents, but the database had no record. ' - error_message += 'The installation log may show this tool dependency to be correctly installed, but due to the ' - error_message += 'missing database record, it is automatically set to Error.' - tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = error_message - else: - error_message = '\nInstallation path %s for tool dependency %s version %s exists, but the expected file %s' % \ - ( str( install_dir ), str( package_name ), str( package_version ), str( fabric_util.INSTALLATION_LOG ) ) - error_message += ' is missing. This indicates an installation error so the tool dependency is being' - error_message += ' prepared for re-installation.' - print error_message - tool_dependency.status = app.model.ToolDependency.installation_status.NEVER_INSTALLED - try: - shutil.rmtree( install_dir ) - except Exception, e: - log.exception( 'Unable to remove installation path %s.', install_dir ) - can_install_tool_dependency = True - sa_session.add( tool_dependency ) - sa_session.flush() + # Notice that we'll throw away the following tool_dependency if it can be installed. + tool_dependency, can_install_tool_dependency = \ + tool_dependency_util.sync_database_with_file_system( app, + tool_shed_repository, + package_name, + package_version, + install_dir, + tool_dependency_type='package' ) else: can_install_tool_dependency = True if can_install_tool_dependency: @@ -775,23 +745,6 @@ tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) return tool_dependency - -# TODO: Move to tool_dependency_util? -def required_repository_package_env( app, package_name, package_version, required_repository ): - """ - Return path to env.sh file in required repository if the required repository has been installed. - """ - env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, - repository_name=required_repository.name, - repository_owner=required_repository.owner, - repository_changeset_revision=required_repository.installed_changeset_revision, - tool_dependency_type='package', - tool_dependency_name=package_name, - tool_dependency_version=package_version ) - env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) - return env_sh_file_path - - def run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=None, **kwd ): """ TODO: Handle this using the fabric api. @@ -846,10 +799,7 @@ tmp_stderr = open( tmp_name, 'rb' ) message = '%s\n' % str( tmp_stderr.read() ) tmp_stderr.close() - try: - os.remove( tmp_name ) - except: - pass + suc.remove_file( tmp_name ) return returncode, message def set_environment( app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ): @@ -935,17 +885,3 @@ for arg in args: parts.append( arg.strip( '/' ) ) return '/'.join( parts ) - - -# TODO: Move to tool_dependency_util? -def __mark_tool_dependency_installed( app, tool_dependency ): - if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, - app.model.ToolDependency.installation_status.INSTALLED ]: - log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ - ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) ) - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLED, - error_message=None, - remove_from_disk=False ) - return tool_dependency diff -r ef33472f0aa296e55fd811357e09366f9cee5467 -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -458,6 +458,7 @@ if index is not None: tool_dependency = tool_dependencies[ index ] if tool_dependency.can_install: + # The database record is currently in a state that allows us to install the package on the file system. try: dependencies_ignored = app.toolbox.dependency_manager and not app.toolbox.dependency_manager.uses_tool_shed_dependencies() if dependencies_ignored: diff -r ef33472f0aa296e55fd811357e09366f9cee5467 -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1521,11 +1521,21 @@ def remove_dir( dir ): """Attempt to remove a directory from disk.""" - if os.path.exists( dir ): - try: - shutil.rmtree( dir ) - except: - pass + if dir: + if os.path.exists( dir ): + try: + shutil.rmtree( dir ) + except: + pass + +def remove_file( file_name ): + """Attempt to remove a file from disk.""" + if file_name: + if os.path.exists( file_name ): + try: + os.remove( dir ) + except: + pass def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple ): """ diff -r ef33472f0aa296e55fd811357e09366f9cee5467 -r cac7a527140e097e6e7f1f5d0fdcf588a8183ece lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -7,6 +7,7 @@ import tool_shed.util.shed_util_common as suc import tool_shed.repository_types.util as rt_util from tool_shed.util import xml_util +from tool_shed.galaxy_install.tool_dependencies import fabric_util log = logging.getLogger( __name__ ) @@ -276,6 +277,18 @@ platform_dict[ 'architecture' ] = machine.lower() return platform_dict +def get_required_repository_package_env_sh_path( app, package_name, package_version, required_repository ): + """Return path to env.sh file in required repository if the required repository has been installed.""" + env_sh_file_dir = get_tool_dependency_install_dir( app=app, + repository_name=required_repository.name, + repository_owner=required_repository.owner, + repository_changeset_revision=required_repository.installed_changeset_revision, + tool_dependency_type='package', + tool_dependency_name=package_name, + tool_dependency_version=package_version ) + env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) + return env_sh_file_path + def get_tool_dependency( trans, id ): """Get a tool_dependency from the database via id""" return trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) ) @@ -368,6 +381,18 @@ sa_session.flush() return tool_dependency +def mark_tool_dependency_installed( app, tool_dependency ): + if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, + app.model.ToolDependency.installation_status.INSTALLED ]: + log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ + ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) ) + tool_dependency = set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLED, + error_message=None, + remove_from_disk=False ) + return tool_dependency + def merge_missing_tool_dependencies_to_installed_container( containers_dict ): """ Merge the list of missing tool dependencies into the list of installed tool dependencies.""" missing_td_container_root = containers_dict.get( 'missing_tool_dependencies', None ) @@ -491,6 +516,72 @@ sa_session.flush() return tool_dependency +def sync_database_with_file_system( app, tool_shed_repository, tool_dependency_name, tool_dependency_version, tool_dependency_install_dir, + tool_dependency_type='package' ): + """ + The installation directory defined by the received tool_dependency_install_dir exists, so check for the presence + of fabric_util.INSTALLATION_LOG. If the files exists, we'll assume the tool dependency is installed, but not + necessarily successfully (it could be in an error state on disk. However, we can justifiably assume here that no + matter the state, an associated database record will exist. + """ + # This method should be reached very rarely. It implies that either the Galaxy environment became corrupted (i.e., + # the database records for installed tool dependencies is not synchronized with tool dependencies on disk) or the Tool + # Shed's install and test framework is running. + sa_session = app.model.context.current + can_install_tool_dependency = False + tool_dependency = get_tool_dependency_by_name_version_type_repository( app, + tool_shed_repository, + tool_dependency_name, + tool_dependency_version, + tool_dependency_type ) + if tool_dependency.status == app.model.ToolDependency.installation_status.INSTALLING: + # The tool dependency is in an Installing state, so we don't want to do anything to it. If the tool + # dependency is being installed by someone else, we don't want to interfere with that. This assumes + # the installation by "someone else" is not hung in an Installing state, which is a weakness if that + # "someone else" never repaired it. + log.debug( 'Skipping installation of tool dependency %s version %s because it has a status of %s' % \ + ( str( tool_dependency.name ), str( tool_dependency.version ), str( tool_dependency.status ) ) ) + else: + # We have a pre-existing installation directory on the file system, but our associated database record is + # in a state that allowed us to arrive here - see the comment in common_install_util.handle_tool_dependencies(). + # At this point, we'll inspect the installation directory to see if we have a "proper installation" and + # if so, synchronize the database record rather than reinstalling the dependency if we're "running_functional_tests". + # If we're not "running_functional_tests, we'll set the tool dependency's installation status to ERROR. + tool_dependency_installation_directory_contents = os.listdir( tool_dependency_install_dir ) + if fabric_util.INSTALLATION_LOG in tool_dependency_installation_directory_contents: + # Since this tool dependency's installation directory contains an installation log, we consider it to be + # installed. In some cases the record may be missing from the database due to some activity outside of + # the control of the Tool Shed. Since a new record was created for it and we don't know the state of the + # files on disk, we will set it to an error state (unless we are running Tool Shed functional tests - see + # below). + log.debug( 'Skipping installation of tool dependency %s version %s because it is installed in %s' % \ + ( str( tool_dependency.name ), str( tool_dependency.version ), str( tool_dependency_install_dir ) ) ) + if app.config.running_functional_tests: + # If we are running functional tests, the state will be set to Installed because previously compiled + # tool dependencies are not deleted by default, from the "install and test" framework.. + tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED + else: + error_message = 'The installation directory for this tool dependency had contents, but the database had no record. ' + error_message += 'The installation log may show this tool dependency to be correctly installed, but due to the ' + error_message += 'missing database record, it is automatically set to Error.' + tool_dependency.status = app.model.ToolDependency.installation_status.ERROR + tool_dependency.error_message = error_message + else: + error_message = '\nInstallation path %s for tool dependency %s version %s exists, but the expected file %s' % \ + ( str( tool_dependency_install_dir ), + str( tool_dependency_name ), + str( tool_dependency_version ), + str( fabric_util.INSTALLATION_LOG ) ) + error_message += ' is missing. This indicates an installation error so the tool dependency is being' + error_message += ' prepared for re-installation.' + print error_message + tool_dependency.status = app.model.ToolDependency.installation_status.NEVER_INSTALLED + suc.remove_dir( tool_dependency_install_dir ) + can_install_tool_dependency = True + sa_session.add( tool_dependency ) + sa_session.flush() + return tool_dependency, can_install_tool_dependency + def tool_dependency_is_orphan( type, name, version, tools ): """ Determine if the combination of the received type, name and version is defined in the <requirement> tag for at least one tool in the Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 02 Dec '13

02 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0b2ecfd14689/ Changeset: 0b2ecfd14689 User: jmchilton Date: 2013-12-02 21:57:00 Summary: Tell nose functions in lib/galaxy/tools/test.py are not unit tests. Affected #: 1 file diff -r cf0d0001893cabb08a01a6d8938f3aa24be4cada -r 0b2ecfd1468979ea94b00c12eaafcac6f330b37e lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -4,6 +4,10 @@ from parameters import basic from parameters import grouping from galaxy.util import string_as_bool +try: + from nose.tools import nottest +except ImportError: + nottest = lambda x: x import logging log = logging.getLogger( __name__ ) @@ -14,6 +18,7 @@ DEFAULT_MAX_SECS = 120 +@nottest def parse_tests_elem(tool, tests_elem): """ Build ToolTestBuilder objects for each "<test>" elements and @@ -196,6 +201,7 @@ return require_file( name, value, extra, self.required_files ) +@nottest def test_data_iter( required_files ): for fname, extra in required_files: data_dict = dict( https://bitbucket.org/galaxy/galaxy-central/commits/ef33472f0aa2/ Changeset: ef33472f0aa2 User: jmchilton Date: 2013-12-02 21:57:00 Summary: Fix test case in test/unit/test_tool_deps.py which fails if modulecmd is unavailable. Affected #: 1 file diff -r 0b2ecfd1468979ea94b00c12eaafcac6f330b37e -r ef33472f0aa296e55fd811357e09366f9cee5467 test/unit/test_tool_deps.py --- a/test/unit/test_tool_deps.py +++ b/test/unit/test_tool_deps.py @@ -293,7 +293,7 @@ def test_config_module_defaults(): with __parse_resolvers('''<dependency_resolvers> - <modules /> + <modules prefetch="false" /></dependency_resolvers> ''') as dependency_resolvers: module_resolver = dependency_resolvers[0] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for missing eggs.require in lib/galaxy/exceptions/__init__.py.
by commits-noreply＠bitbucket.org 02 Dec '13

02 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cf0d0001893c/ Changeset: cf0d0001893c User: dan Date: 2013-12-02 20:48:30 Summary: Fix for missing eggs.require in lib/galaxy/exceptions/__init__.py. Affected #: 1 file diff -r cd94f9721265741d448a225df511141190049f34 -r cf0d0001893cabb08a01a6d8938f3aa24be4cada lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -1,6 +1,10 @@ """ Custom exceptions for Galaxy """ + +from galaxy import eggs +eggs.require( "Paste" ) + from paste import httpexceptions class MessageException( Exception ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 02 Dec '13

02 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/44acfec11d87/ Changeset: 44acfec11d87 User: jmchilton Date: 2013-11-27 17:12:48 Summary: Patch from Peter Cock. Allow overriding composite type main file in archives. Affected #: 1 file diff -r 372ff609235643994e50f1502fb9c73d37a3f97f -r 44acfec11d87f2efc38bccb2b3333e86b9d96667 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -199,6 +199,29 @@ out = "Can't create peek %s" % str( exc ) return out + def _archive_main_file(self, archive, outfname, data_filename): + """Called from _archive_composite_dataset to add central file to archive. + + Unless subclassed, this will add the main dataset file (argument data_filename) + to the archive, as an HTML file with its filename derived from the dataset name + (argument outfname). + + Returns a tuple of boolean, string, string: (error, msg, messagetype) + """ + error, msg, messagetype = False, "", "" + htmlname = os.path.splitext(outfname)[0] + if not htmlname.endswith(ext): + htmlname = '%s_%s' % (htmlname, ext) + archname = '%s.html' % htmlname # fake the real nature of the html file + try: + archive.add(data_filename, archname) + except IOError: + error = True + log.exception("Unable to add composite parent %s to temporary library download archive" % data_filename) + msg = "Unable to create archive for download, please report this error" + messagetype = "error" + return error, msg, messagetype + def _archive_composite_dataset( self, trans, data=None, **kwd ): # save a composite object into a compressed archive for downloading params = util.Params( kwd ) @@ -233,33 +256,25 @@ messagetype = 'error' if not error: current_user_roles = trans.get_current_user_roles() - ext = data.extension path = data.file_name fname = os.path.split(path)[-1] efp = data.extra_files_path - htmlname = os.path.splitext(outfname)[0] - if not htmlname.endswith(ext): - htmlname = '%s_%s' % (htmlname,ext) - archname = '%s.html' % htmlname # fake the real nature of the html file - try: - archive.add(data.file_name,archname) - except IOError: - error = True - log.exception( "Unable to add composite parent %s to temporary library download archive" % data.file_name) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' - for root, dirs, files in os.walk(efp): - for fname in files: - fpath = os.path.join(root,fname) - rpath = os.path.relpath(fpath,efp) - try: - archive.add( fpath,rpath ) - except IOError: - error = True - log.exception( "Unable to add %s to temporary library download archive" % rpath) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' - continue + #Add any central file to the archive, + error, msg, messagetype = self._archive_main_file(archive, outfname, path) + if not error: + #Add any child files to the archive, + for root, dirs, files in os.walk(efp): + for fname in files: + fpath = os.path.join(root,fname) + rpath = os.path.relpath(fpath,efp) + try: + archive.add( fpath,rpath ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive" % rpath) + msg = "Unable to create archive for download, please report this error" + messagetype = 'error' + continue if not error: if params.do_action == 'zip': archive.close() https://bitbucket.org/galaxy/galaxy-central/commits/cd94f9721265/ Changeset: cd94f9721265 User: jmchilton Date: 2013-12-02 19:40:43 Summary: Fix default behavior of composite archival broken with previous changeset. Other small tweaks this implementation. Affected #: 1 file diff -r 44acfec11d87f2efc38bccb2b3333e86b9d96667 -r cd94f9721265741d448a225df511141190049f34 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -199,7 +199,7 @@ out = "Can't create peek %s" % str( exc ) return out - def _archive_main_file(self, archive, outfname, data_filename): + def _archive_main_file(self, archive, display_name, data_filename): """Called from _archive_composite_dataset to add central file to archive. Unless subclassed, this will add the main dataset file (argument data_filename) @@ -209,10 +209,7 @@ Returns a tuple of boolean, string, string: (error, msg, messagetype) """ error, msg, messagetype = False, "", "" - htmlname = os.path.splitext(outfname)[0] - if not htmlname.endswith(ext): - htmlname = '%s_%s' % (htmlname, ext) - archname = '%s.html' % htmlname # fake the real nature of the html file + archname = '%s.html' % display_name # fake the real nature of the html file try: archive.add(data_filename, archname) except IOError: @@ -256,11 +253,17 @@ messagetype = 'error' if not error: current_user_roles = trans.get_current_user_roles() + ext = data.extension path = data.file_name fname = os.path.split(path)[-1] efp = data.extra_files_path #Add any central file to the archive, - error, msg, messagetype = self._archive_main_file(archive, outfname, path) + + display_name = os.path.splitext(outfname)[0] + if not display_name.endswith(ext): + display_name = '%s_%s' % (display_name, ext) + + error, msg, messagetype = self._archive_main_file(archive, display_name, path) if not error: #Add any child files to the archive, for root, dirs, files in os.walk(efp): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Grids: Fix unescaping strings
by commits-noreply＠bitbucket.org 02 Dec '13

02 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/372ff6092356/ Changeset: 372ff6092356 User: guerler Date: 2013-12-02 19:07:17 Summary: Grids: Fix unescaping strings Affected #: 1 file diff -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 -r 372ff609235643994e50f1502fb9c73d37a3f97f templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -403,9 +403,10 @@ value = column_settings['value'] inbound = column_settings['inbound'] - # check if formatting is defined - value = str(value).replace('//', '/') - + # unescape value + if isinstance(value, unicode): + value = value.replace('//', '/') + # Attach popup menu? id = "" cls = "" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Update LWR client through LWR revision acecc74f7016.
by commits-noreply＠bitbucket.org 01 Dec '13

01 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/752929cea6d3/ Changeset: 752929cea6d3 User: jmchilton Date: 2013-12-01 13:14:32 Summary: Update LWR client through LWR revision acecc74f7016. Mostly small modifications related Python 3 compat. (no iteritems, diff. StringIO, exception syntax, urllib diffs,) and improved handling of unicode data. Affected #: 6 files diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/action_mapper.py --- a/lib/galaxy/jobs/runners/lwr_client/action_mapper.py +++ b/lib/galaxy/jobs/runners/lwr_client/action_mapper.py @@ -21,7 +21,7 @@ >>> from tempfile import NamedTemporaryFile >>> from os import unlink >>> f = NamedTemporaryFile(delete=False) - >>> f.write(json_string) + >>> write_result = f.write(json_string.encode('UTF-8')) >>> f.close() >>> class MockClient(): ... default_file_action = 'none' @@ -30,23 +30,23 @@ >>> mapper = FileActionMapper(MockClient()) >>> unlink(f.name) >>> # Test first config line above, implicit path prefix mapper - >>> mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input') - ('none',) + >>> mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input')[0] == u'none' + True >>> # Test another (2nd) mapper, this one with a different action - >>> mapper.action('/galaxy/data/files/000/dataset_1.dat', 'input') - ('transfer',) + >>> mapper.action('/galaxy/data/files/000/dataset_1.dat', 'input')[0] == u'transfer' + True >>> # Always at least copy work_dir outputs. - >>> mapper.action('/opt/galaxy/database/working_directory/45.sh', 'work_dir') - ('copy',) + >>> mapper.action('/opt/galaxy/database/working_directory/45.sh', 'work_dir')[0] == u'copy' + True >>> # Test glob mapper (matching test) - >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam', 'input') - ('copy',) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam', 'input')[0] == u'copy' + True >>> # Test glob mapper (non-matching test) - >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam.bai', 'input') - ('none',) + >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam.bai', 'input')[0] == u'none' + True >>> # Regex mapper test. - >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'input') - ('copy',) + >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'input')[0] == u'copy' + True """ def __init__(self, client): diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/destination.py --- a/lib/galaxy/jobs/runners/lwr_client/destination.py +++ b/lib/galaxy/jobs/runners/lwr_client/destination.py @@ -51,9 +51,10 @@ >>> destination_params = {"private_token": "12345", "submit_native_specification": "-q batch"} >>> result = submit_params(destination_params) - >>> result.items() - [('native_specification', '-q batch')] + >>> result + {'native_specification': '-q batch'} """ - return dict([(key[len(SUBMIT_PREFIX):], value) - for key, value in (destination_params or {}).iteritems() + destination_params = destination_params or {} + return dict([(key[len(SUBMIT_PREFIX):], destination_params[key]) + for key in destination_params if key.startswith(SUBMIT_PREFIX)]) diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -5,8 +5,18 @@ from queue import Queue from threading import Thread from os import getenv -from urllib import urlencode -from StringIO import StringIO +try: + from urllib import urlencode +except ImportError: + from urllib.parse import urlencode +try: + from StringIO import StringIO as BytesIO +except ImportError: + from io import BytesIO +try: + from six import text_type +except ImportError: + from galaxy.util import unicodify as text_type from .client import Client, InputCachingClient from .transport import get_transport @@ -27,10 +37,10 @@ """ def __init__(self, **kwds): if 'job_manager' in kwds: - self.job_manager_interface_class = LocalJobManagerInterface + self.job_manager_interface_class = LocalLwrInterface self.job_manager_interface_args = dict(job_manager=kwds['job_manager'], file_cache=kwds['file_cache']) else: - self.job_manager_interface_class = HttpJobManagerInterface + self.job_manager_interface_class = HttpLwrInterface transport_type = kwds.get('transport_type', None) transport = get_transport(transport_type) self.job_manager_interface_args = dict(transport=transport) @@ -55,7 +65,11 @@ return self.client_class(destination_params, job_id, job_manager_interface, **self.extra_client_kwds) def __parse_destination_params(self, destination_params): - if isinstance(destination_params, str) or isinstance(destination_params, unicode): + try: + unicode_type = unicode + except NameError: + unicode_type = str + if isinstance(destination_params, str) or isinstance(destination_params, unicode_type): destination_params = url_to_destination_params(destination_params) return destination_params @@ -76,7 +90,7 @@ """ -class HttpJobManagerInterface(object): +class HttpLwrInterface(object): def __init__(self, destination_params, transport): self.transport = transport @@ -92,12 +106,13 @@ def __build_url(self, command, args): if self.private_key: args["private_key"] = self.private_key - data = urlencode(args) + arg_bytes = dict([(k, text_type(args[k]).encode('utf-8')) for k in args]) + data = urlencode(arg_bytes) url = self.remote_host + command + "?" + data return url -class LocalJobManagerInterface(object): +class LocalLwrInterface(object): def __init__(self, destination_params, job_manager, file_cache): self.job_manager = job_manager @@ -113,6 +128,7 @@ } def execute(self, command, args={}, data=None, input_path=None, output_path=None): + # If data set, should be unicode (on Python 2) or str (on Python 3). from lwr import routes from lwr.framework import build_func_args controller = getattr(routes, command) @@ -129,9 +145,9 @@ def __build_body(self, data, input_path): if data is not None: - return StringIO(data) + return BytesIO(data.encode('utf-8')) elif input_path is not None: - return open(input_path, 'r') + return open(input_path, 'rb') else: return None @@ -188,4 +204,4 @@ int_val = int(val) return int_val -__all__ = [ClientManager, HttpJobManagerInterface] +__all__ = [ClientManager, HttpLwrInterface] diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/stager.py --- a/lib/galaxy/jobs/runners/lwr_client/stager.py +++ b/lib/galaxy/jobs/runners/lwr_client/stager.py @@ -1,6 +1,7 @@ from os.path import abspath, basename, join, exists from os import listdir, sep from re import findall +from io import open from .action_mapper import FileActionMapper @@ -24,22 +25,24 @@ >>> import tempfile >>> tf = tempfile.NamedTemporaryFile() >>> def setup_inputs(tf): - ... open(tf.name, "w").write("world /path/to/input the rest") - ... inputs = JobInputs("hello /path/to/input", [tf.name]) + ... open(tf.name, "w").write(u"world /path/to/input the rest") + ... inputs = JobInputs(u"hello /path/to/input", [tf.name]) ... return inputs >>> inputs = setup_inputs(tf) - >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') - >>> inputs.rewritten_command_line - 'hello C:\\\\input' - >>> inputs.rewritten_config_files[tf.name] - 'world C:\\\\input the rest' + >>> inputs.rewrite_paths(u"/path/to/input", u'C:\\input') + >>> inputs.rewritten_command_line == u'hello C:\\\\input' + True + >>> inputs.rewritten_config_files[tf.name] == u'world C:\\\\input the rest' + True >>> tf.close() >>> tf = tempfile.NamedTemporaryFile() >>> inputs = setup_inputs(tf) - >>> inputs.find_referenced_subfiles('/path/to') - ['/path/to/input'] + >>> inputs.find_referenced_subfiles('/path/to') == [u'/path/to/input'] + True >>> inputs.path_referenced('/path/to') True + >>> inputs.path_referenced(u'/path/to') + True >>> inputs.path_referenced('/path/to/input') True >>> inputs.path_referenced('/path/to/notinput') @@ -92,7 +95,7 @@ self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) def __rewrite_config_files(self, local_path, remote_path): - for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): + for config_file, rewritten_contents in self.rewritten_config_files.items(): self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) def __items(self): @@ -140,7 +143,7 @@ For each file that has been transferred and renamed, updated command_line and configfiles to reflect that rewrite. """ - for local_path, remote_path in self.file_renames.iteritems(): + for local_path, remote_path in self.file_renames.items(): self.job_inputs.rewrite_paths(local_path, remote_path) def __action(self, path, type): @@ -283,7 +286,7 @@ self.transfer_tracker.rewrite_input_paths() def __upload_rewritten_config_files(self): - for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): + for config_file, new_config_contents in self.job_inputs.rewritten_config_files.items(): self.client.put_file(config_file, input_type='config', contents=new_config_contents) def get_rewritten_command_line(self): @@ -304,7 +307,7 @@ try: action = action_mapper.action(output_file, 'output') client.fetch_work_dir_output(source_file, working_directory, output_file, action[0]) - except Exception, e: + except Exception as e: download_failure_exceptions.append(e) # Remove from full output_files list so don't try to download directly. output_files.remove(output_file) @@ -312,7 +315,7 @@ try: action = action_mapper.action(output_file, 'output') client.fetch_output(output_file, working_directory=working_directory, action=action[0]) - except Exception, e: + except Exception as e: download_failure_exceptions.append(e) return __clean(download_failure_exceptions, cleanup_job, client) @@ -340,9 +343,9 @@ def _read(path): """ Utility method to quickly read small files (config files and tool - wrappers) into memory as strings. + wrappers) into memory as bytes. """ - input = open(path, "r") + input = open(path, "r", encoding="utf-8") try: return input.read() finally: diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/transport/curl.py --- a/lib/galaxy/jobs/runners/lwr_client/transport/curl.py +++ b/lib/galaxy/jobs/runners/lwr_client/transport/curl.py @@ -1,4 +1,7 @@ -from cStringIO import StringIO +try: + from cStringIO import StringIO +except ImportError: + from io import StringIO try: from pycurl import Curl except: @@ -25,6 +28,8 @@ c.setopt(c.INFILESIZE, filesize) if data: c.setopt(c.POST, 1) + if type(data).__name__ == 'unicode': + data = data.encode('UTF-8') c.setopt(c.POSTFIELDS, data) c.perform() if not output_path: diff -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 -r 752929cea6d37423c14f46f317ef3815cfc3c3d0 lib/galaxy/jobs/runners/lwr_client/transport/standard.py --- a/lib/galaxy/jobs/runners/lwr_client/transport/standard.py +++ b/lib/galaxy/jobs/runners/lwr_client/transport/standard.py @@ -3,16 +3,23 @@ """ from __future__ import with_statement import mmap -import urllib2 +try: + from urllib2 import urlopen +except ImportError: + from urllib.request import urlopen +try: + from urllib2 import Request +except ImportError: + from urllib.request import Request class Urllib2Transport(object): def _url_open(self, request, data): - return urllib2.urlopen(request, data) + return urlopen(request, data) def execute(self, url, data=None, input_path=None, output_path=None): - request = urllib2.Request(url=url, data=data) + request = Request(url=url, data=data) input = None try: if input_path: @@ -26,7 +33,7 @@ with open(output_path, 'wb') as output: while True: buffer = response.read(1024) - if buffer == "": + if not buffer: break output.write(buffer) return response Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 30 Nov '13

30 Nov '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/842d13d7925c/ Changeset: 842d13d7925c User: jgoecks Date: 2013-11-29 17:41:26 Summary: Trackster: move static CSS settings out of JavaScript and into CSS file. Affected #: 3 files diff -r 8b613225f1def637af4774b860578a77a7fb0fe4 -r 842d13d7925c67764a0099a445b133392a0b0e13 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -32,8 +32,7 @@ var moveable = function(element, handle_class, container_selector, element_js_obj) { // HACK: set default value for container selector. container_selector = ".group"; - var css_border_props = {}; - + // Register element with its object. html_elt_js_obj_dict[element.attr("id")] = element_js_obj; @@ -130,14 +129,9 @@ html_elt_js_obj_dict[parent.attr("id")].move_drawable(this_obj, (d.deltaY > 0 ? i-1 : i) ); } }).bind("dragstart", function() { - css_border_props["border-top"] = element.css("border-top"); - css_border_props["border-bottom"] = element.css("border-bottom"); - $(this).css({ - "border-top": "1px solid blue", - "border-bottom": "1px solid blue" - }); + $(this).addClass('dragging'); }).bind("dragend", function() { - $(this).css(css_border_props); + $(this).removeClass('dragging'); }); }; @@ -236,7 +230,7 @@ this.container_div.append(this.header_div); // Icons container. - this.icons_div = $("<div/>").css("float", "left").hide().appendTo(this.header_div); + this.icons_div = $("<div/>").addClass('track-icons').hide().appendTo(this.header_div); this.build_action_icons(this.action_icons_def); this.header_div.append( $("<div style='clear: both'/>") ); @@ -930,7 +924,7 @@ // Top container for things that are fixed at the top this.top_container = $("<div/>").addClass("top-container").appendTo(parent_element); // Browser content, primary tracks are contained in here - this.browser_content_div = $("<div/>").addClass("content").css("position", "relative").appendTo(parent_element); + this.browser_content_div = $("<div/>").addClass("content").appendTo(parent_element); // Bottom container for things that are fixed at the bottom this.bottom_container = $("<div/>").addClass("bottom-container").appendTo(parent_element); // Label track fixed at top @@ -967,7 +961,7 @@ this.default_overview_height = this.overview_box.height(); this.nav_controls = $("<div/>").addClass("nav-controls").appendTo(this.nav); - this.chrom_select = $("<select/>").attr({ "name": "chrom"}).css("width", "15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls); + this.chrom_select = $("<select/>").attr({ "name": "chrom"}).addClass('chrom-nav').append("<option value=''>Loading</option>").appendTo(this.nav_controls); var submit_nav = function(e) { if (e.type === "focusout" || (e.keyCode || e.which) === 13 || (e.keyCode || e.which) === 27 ) { if ((e.keyCode || e.which) !== 27) { // Not escape key @@ -1708,7 +1702,7 @@ // Add buttons for running on dataset, region. var run_tool_row = $("<div>").addClass("param-row").appendTo(parent_div); var run_on_dataset_button = $("<input type='submit'>").attr("value", "Run on complete dataset").appendTo(run_tool_row); - var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").css("margin-left", "3em").appendTo(run_tool_row); + var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").appendTo(run_tool_row); run_on_region_button.click( function() { // Run tool to create new track. self.run_on_region(); @@ -2027,7 +2021,10 @@ else if ( param.type === 'color' ) { var container_div = $("<div/>").appendTo(row), - input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left") + input = $('<input/>').attr({ + id: id, + name: id + }).val( value ).addClass('color-input') .appendTo(container_div).click(function(e) { // Hide other pickers. $(".tooltip").removeClass( "in" ); @@ -2517,7 +2514,7 @@ }, build_container_div: function () { - return $("<div/>").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); + return $("<div/>").addClass('track').attr("id", "track_" + this.id); }, build_header_div: function() { @@ -3532,7 +3529,6 @@ while ( position < view.high ) { var screenPosition = ( position - view.low ) / range * width; new_div.append( $("<div/>").addClass('label').text(commatize( position )).css( { - // Reduce by one to account for border left: screenPosition })); position += tickDistance; diff -r 8b613225f1def637af4774b860578a77a7fb0fe4 -r 842d13d7925c67764a0099a445b133392a0b0e13 static/style/blue/trackster.css --- a/static/style/blue/trackster.css +++ b/static/style/blue/trackster.css @@ -1,14 +1,14 @@ .viewport-container{overflow-x:hidden;overflow-y:auto;background:white} .trackster-nav-container{width:100%;height:0;text-align:center} .trackster-nav{padding:0 0;color:#333;font-weight:bold;background:#cccccc;position:relative;display:inline-block;top:-2em;background:transparent;border:none} -.content{font:10px verdana} +.chrom-nav{width:15em} +.content{font:10px verdana;position:relative} .nav-controls{text-align:center;padding:1px 0}.nav-controls input{margin:0 5px} #zoom-in,#zoom-out{display:inline-block;height:16px;width:16px;margin-bottom:-3px;cursor:pointer} #zoom-out{background:transparent url(../images/fugue/magnifier-zoom-out.png) center center no-repeat} #zoom-in{margin-left:10px;background:transparent url(../images/fugue/magnifier-zoom.png) center center no-repeat} .nav-input{font-size:12px;width:30em;z-index:2} .location{display:inline-block;width:15em;margin:0 10px} -.draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px} .intro{z-index:2;margin-left:auto;margin-right:auto;color:#555;text-align:center;font-size:16px}.intro .action-button{background-color:#CCC;margin-top:10px;padding:1em;text-decoration:underline} .overview{width:100%;margin:0px;color:white} .overview-viewport{position:relative;height:14px;background:white;margin:0} @@ -28,7 +28,7 @@ .overlay{position:absolute;left:0;top:0} .track-tile{position:absolute;background:white}.track-tile canvas{position:relative;z-index:1} .tile-message{border-bottom:solid 1px red;text-align:center;color:red;background-color:white} -.track{border-bottom:1px solid #bbb}.track.error{background-color:#ECB4AF;background-image:none} +.track{position:relative;border-bottom:1px solid #bbb}.track.error{background-color:#ECB4AF;background-image:none} .track.nodata .track-content{background-color:white;background-image:none} .track.pending .track-content{background-color:white;background-image:none} .track-content{text-align:center;position:relative;min-height:20px;padding:0px 0px 1px 0px} @@ -40,7 +40,8 @@ .right-float{float:right;margin-left:5px} .top-labeltrack{position:relative;border-bottom:solid #999 1px} .nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px} -input{font:10px verdana}input[type="submit"]{padding:0px;font-size:inherit} +input{font:10px verdana}input[type="submit"]{padding:0px;margin-right:20px;font-size:inherit} +input.color-input{float:left} .dynamic-tool,.filters{padding-top:18px;padding-bottom:0.5em;margin-left:0.25em} .dynamic-tool{width:410px} .filters{float:left;margin:1em;width:60%;position:relative} @@ -53,6 +54,7 @@ .param-label{float:left;font-weight:bold;padding-top:0.2em;width:50%} .menu-button{margin:0px 4px 0px 4px} .exclamation{background:transparent url(../images/fugue/exclamation.png) no-repeat;margin-left:5em} +.track-icons{float:left} .icon-button.bookmarks{background:transparent url('../images/fugue/bookmarks-bw.png') no-repeat}.icon-button.bookmarks:hover{background:transparent url('../images/fugue/bookmarks.png') no-repeat} .icon-button.layers-stack{background:transparent url('../images/fugue/layers-stack-bw.png') no-repeat}.icon-button.layers-stack:hover{background:transparent url('../images/fugue/layers-stack.png') no-repeat} .icon-button.hammer{background:transparent url('../images/fugue/hammer-bw.png') no-repeat}.icon-button.hammer:hover{background:transparent url('../images/fugue/hammer.png') no-repeat} @@ -77,3 +79,5 @@ .feature-popup{position:absolute;z-index:2;padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);background-position:top center} .feature-popup-inner{padding:5px 8px 4px 8px;background-color:black;color:white} .zoom-area{position:absolute;top:0px;background-color:#ccf;opacity:0.5;z-index:2} +.draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px} +.dragging{border:1px solid blue} diff -r 8b613225f1def637af4774b860578a77a7fb0fe4 -r 842d13d7925c67764a0099a445b133392a0b0e13 static/style/src/less/trackster.less --- a/static/style/src/less/trackster.less +++ b/static/style/src/less/trackster.less @@ -31,8 +31,13 @@ border: none; } +.chrom-nav { + width: 15em; +} + .content { font: 10px verdana; + position: relative; } .nav-controls { @@ -72,15 +77,6 @@ margin: 0 10px; } -.draghandle { - margin-top: 2px; - cursor: move; - float: left; - background: transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat; - width: 10px; - height: 12px; -} - .intro { z-index: @overlay-index; /* margin-top: 200px;*/ @@ -244,6 +240,8 @@ } .track { + position: relative; + // Separates tracks. border-bottom: 1px solid @separator-color; @@ -340,8 +338,13 @@ // Override Galaxy defaults to make a smaller button. &[type="submit"] { padding: 0px; + margin-right: 20px; font-size: inherit; } + + &.color-input { + float: left; + } } .dynamic-tool, .filters { @@ -415,6 +418,10 @@ margin-left: 5em; } +.track-icons { + float: left +} + // Defines icons that change from black/white to normal on hover. Note that the images // are required to exist in the location specified. // TODO: make images into spritemap. @@ -523,4 +530,19 @@ background-color: #ccf; opacity: 0.5; z-index: @overlay-index; +} + +.draghandle { + margin-top: 2px; + cursor: move; + float: left; + background: transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat; + width: 10px; + height: 12px; +} + +// Highlight for element(s) being dragged. This definition must be after definition of draggable +// elements (e.g. track, group) in order to take precedence. +.dragging { + border: 1px solid blue; } \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/c2d705f7b50a/ Changeset: c2d705f7b50a User: jgoecks Date: 2013-11-30 23:00:01 Summary: Trackster: (a) use colors to denote track state and (b) add and use function to show messages. Affected #: 3 files diff -r 842d13d7925c67764a0099a445b133392a0b0e13 -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2667,23 +2667,35 @@ }, /** + * Remove visualization content and display message. + */ + show_message: function(msg_html) { + this.tiles_div.remove(); + return $('<span/>').addClass('message').html(msg_html).appendTo(this.content_div); + }, + + /** * Initialize and draw the track. */ init: function(retry) { + // FIXME: track should have a 'state' attribute that is checked on load; this state attribute should be + // used in this function to determine what action(s) to take. + var track = this; track.enabled = false; track.tile_cache.clear(); track.data_manager.clear(); - track.tiles_div.css("height", "auto"); /* if (!track.content_div.text()) { track.content_div.text(DATA_LOADING); } */ // Remove old track content (e.g. tiles, messages). - track.tiles_div.text('').children().remove(); + track.content_div.children().remove(); track.container_div.removeClass("nodata error pending"); - + + track.tiles_div = $("<div/>").addClass("tiles").appendTo(track.content_div); + // // Tracks with no dataset id are handled differently. // FIXME: is this really necessary? @@ -2705,16 +2717,16 @@ if (!result || result === "error" || result.kind === "error") { // Dataset is in error state. track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); + var msg_elt = track.show_message(DATA_ERROR); if (result.message) { // Add links to (a) show error and (b) try again. - track.content_div.append( + msg_elt.append( $("<a href='javascript:void(0);'></a>").text("View error").click(function() { Galaxy.modal.show({title: "Trackster Error", body: "<pre>" + result.message + "</pre>", buttons : {'Close' : function() { Galaxy.modal.hide(); } } }); }) ); - track.content_div.append( $('<span/>').text(' ') ); - track.content_div.append( + msg_elt.append( $('<span/>').text(' ') ); + msg_elt.append( $("<a href='javascript:void(0);'></a>").text("Try again").click(function() { track.init(true); }) @@ -2723,15 +2735,15 @@ } else if (result === "no converter") { track.container_div.addClass("error"); - track.tiles_div.text(DATA_NOCONVERTER); + track.show_message(DATA_NOCONVERTER); } else if (result === "no data" || (result.data !== undefined && (result.data === null || result.data.length === 0))) { track.container_div.addClass("nodata"); - track.tiles_div.text(DATA_NONE); + track.show_message(DATA_NONE); } else if (result === "pending") { track.container_div.addClass("pending"); - track.tiles_div.html(DATA_PENDING); + track.show_message(DATA_PENDING); //$("<img/>").attr("src", image_path + "/yui/rel_interstitial_loading.gif").appendTo(track.tiles_div); setTimeout(function() { track.init(); }, track.data_query_wait); } diff -r 842d13d7925c67764a0099a445b133392a0b0e13 -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 static/style/blue/trackster.css --- a/static/style/blue/trackster.css +++ b/static/style/blue/trackster.css @@ -20,7 +20,7 @@ .yaxislabel{z-index:2;position:absolute;right:20px} .yaxislabel.bottom{bottom:2px} .group-handle{cursor:move;float:left;background:#eee url('../images/tracks/block.png');width:12px;height:12px} -.group{min-height:20px;border-top:1px solid #bbb;border-bottom:1px solid #bbb}.group>.track-header{position:relative;float:left} +.group{min-height:20px;border-top:1px solid #888;border-bottom:1px solid #888}.group>.track-header{position:relative;float:left} .track-header{height:16px;position:absolute;z-index:2;background-color:rgba(1,1,1,0.1);border-radius:5px;padding:0px 2px;text-align:left;margin:2px;}.track-header:hover{background-color:#DDDDDD} .track-header .menubutton{margin-left:0px} .track-name{float:left;margin-top:2px} @@ -28,10 +28,10 @@ .overlay{position:absolute;left:0;top:0} .track-tile{position:absolute;background:white}.track-tile canvas{position:relative;z-index:1} .tile-message{border-bottom:solid 1px red;text-align:center;color:red;background-color:white} -.track{position:relative;border-bottom:1px solid #bbb}.track.error{background-color:#ECB4AF;background-image:none} -.track.nodata .track-content{background-color:white;background-image:none} -.track.pending .track-content{background-color:white;background-image:none} -.track-content{text-align:center;position:relative;min-height:20px;padding:0px 0px 1px 0px} +.track{position:relative;border-bottom:1px solid #888}.track.error{background:#ECB4AF} +.track.nodata{background:#EEEEEE} +.track.pending{background:#FFFFCC} +.track-content{text-align:center;position:relative;min-height:20px;padding:0px 0px 1px 0px}.track-content .message{position:relative;top:4px} .loading{min-height:100px} .label-track{font-size:10px;border:none;padding:0;margin:0;height:1.5em;overflow:hidden}.label-track .label-container{position:relative;height:1.3em} .label-track .label{position:absolute;border-left:solid #999 1px;padding:1px;padding-bottom:2px;display:inline-block} diff -r 842d13d7925c67764a0099a445b133392a0b0e13 -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 static/style/src/less/trackster.less --- a/static/style/src/less/trackster.less +++ b/static/style/src/less/trackster.less @@ -3,7 +3,7 @@ @overlay-index: @base-index + 1; @track-header-height: 16px; @min-track-height: (@track-header-height + 4); -@separator-color: #BBB; +@separator-color: #888; .viewport-container { overflow-x: hidden; @@ -246,22 +246,15 @@ border-bottom: 1px solid @separator-color; &.error { - background-color: #ECB4AF; - background-image: none; + background: #ECB4AF; } &.nodata { - .track-content { - background-color: white; - background-image: none; - } + background: #EEEEEE; } &.pending { - .track-content { - background-color: white; - background-image: none; - } + background: #FFFFCC; } } @@ -270,6 +263,12 @@ position: relative; min-height: @min-track-height; padding: 0px 0px 1px 0px; + + .message { + position: relative; + // To vertically center message in track: + top: 4px; + } } .loading { https://bitbucket.org/galaxy/galaxy-central/commits/9a5a8d18cd16/ Changeset: 9a5a8d18cd16 User: jgoecks Date: 2013-11-30 23:00:44 Summary: Automated merge of local changesets with default branch. Affected #: 14 files diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3471,6 +3471,29 @@ def can_reinstall_or_activate( self ): return self.deleted + @property + def installing( self ): + """ + Used to determine if tool dependencies can denote this repository as + installing. + """ + return self.status not in [ self.installation_status.DEACTIVATED, + self.installation_status.UNINSTALLED, + self.installation_status.ERROR, + self.installation_status.INSTALLED, + self.installation_status.NEW, + ] + + @property + def installation_complete( self ): + """ + Used to determine if tool dependency installations can proceed. + Installed artifacts must be available on disk. + """ + return self.status in [ self.installation_status.DEACTIVATED, + self.installation_status.INSTALLED, + ] + def to_dict( self, view='collection', value_mapper=None ): if value_mapper is None: value_mapper = {} diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -58,6 +58,8 @@ for p in job.parameters: out[p.name] = p.value for in_d in job.input_datasets: + if not in_d.dataset: + continue if follow: out[in_d.name] = self._get_record(trans, in_d.dataset, follow) else: diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -107,10 +107,9 @@ skip_tool_test = kwd.get( 'skip_tool_test', None ) if skip_tool_test is not None: skip_tool_test = util.string_as_bool( skip_tool_test ) + if skip_tool_test: skipped_metadata_ids_subquery = select( [ trans.app.model.SkipToolTest.table.c.repository_metadata_id ] ) - if skip_tool_test: - clause_list.append( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) ) - else: + if skipped_metadata_ids_subquery: clause_list.append( not_( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) ) ) # Generate and execute the query. try: diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -390,7 +390,7 @@ with lcd( current_dir ): with settings( warn_only=True ): for tarball_name in tarball_names: - cmd = '''export PATH=$PATH:$R_HOME/bin && export R_LIBS=$INSTALL_DIR && + cmd = '''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS; && Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % ( str( tarball_name ) ) cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) @@ -432,24 +432,24 @@ gem, gem_version = ruby_package_tup if os.path.isfile( gem ): # we assume a local shipped gem file - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install --local %s''' % ( gem ) elif gem.find( '://' ) != -1: # We assume a URL to a gem file. url = gem gem_name = url.split( '/' )[ -1 ] td_common_util.url_download( work_dir, gem_name, url, extract=False ) - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install --local %s ''' % ( gem_name ) else: # gem file from rubygems.org with or without version number if gem_version: # version number was specified - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install %s --version "=%s"''' % ( gem, gem_version) else: # no version number given - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install %s''' % ( gem ) cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) @@ -490,7 +490,7 @@ for perl_package in perl_packages: # If set to a true value then MakeMaker's prompt function will always # return the default without waiting for user input. - cmd = '''export PERL_MM_USE_DEFAULT=1 && ''' + cmd = '''PERL_MM_USE_DEFAULT=1; export PERL_MM_USE_DEFAULT; ''' if perl_package.find( '://' ) != -1: # We assume a URL to a gem file. url = perl_package diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -40,6 +40,70 @@ raise Exception( message ) return None + +def find_complex_dependency_package( app, dependent_install_dir, required_install_dir, tool_shed_repository, required_repository, package_name, package_version, tool_dependencies_config ): + """ + """ + tool_dependencies = [] + if not os.path.exists( dependent_install_dir ): + os.makedirs( dependent_install_dir ) + env_file = None + if tool_dependencies_config: + required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config ) + if required_td_tree: + required_td_root = required_td_tree.getroot() + for required_td_elem in required_td_root: + # Find the appropriate package name and version. + if required_td_elem.tag == 'package': + # <package name="bwa" version="0.5.9"> + required_td_package_name = required_td_elem.get( 'name', None ) + required_td_package_version = required_td_elem.get( 'version', None ) + if required_td_package_name == package_name and required_td_package_version == package_version: + tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=package_name, + version=package_version, + type='package', + status=app.model.ToolDependency.installation_status.NEVER_INSTALLED, + set_status=True ) + + if required_repository.installing: + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLING ) + # What happens if dependent repository fails or is + # uninstalled during this process. + env_file = required_repository_package_env( app, package_name, package_version, required_repository ) + if required_repository.installation_complete: + if not os.path.exists( env_file ): + error_message = 'env.sh file %s for package %s in dependendent repository could not be found. Required repository has status %s.' % ( package_name, env_file, required_repository.status ) + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency, + error_message, + remove_installation_path=False ) + else: + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLED ) + else: + # Ekk - handling tool depednencies for a dependent + # repository that is not installed. + # + # Go ahead a return the env.sh file - Galaxy will + # proceed to create an invalid symbolic link. + # This is subtle-ly different than the previous + # behavior which would have recreated an env.sh + # from the the required repository's + # tool_dependencies.xml but since it was not + # installed all of the values inside would be + # invalid path modifications. Either way, this file + # is junk until the required repository is + # installed properly. + pass + tool_dependencies.append( tool_dependency ) + return tool_dependencies, env_file + + def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ): """Return the absolute path to a specified disk file contained in a repository.""" stripped_file_name = strip_path( file_name ) @@ -91,6 +155,7 @@ text = common_util.tool_shed_get( app, tool_shed_url, url ) return text + def handle_complex_repository_dependency_for_package( app, elem, package_name, package_version, tool_shed_repository ): handled_tool_dependencies = [] tool_shed = elem.attrib[ 'toolshed' ] @@ -125,8 +190,7 @@ tool_dependency_version=package_version ) # Set this dependent repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package. # We can get everything we need from the discovered installed required_repository. - if required_repository.status in [ app.model.ToolShedRepository.installation_status.DEACTIVATED, - app.model.ToolShedRepository.installation_status.INSTALLED ]: + if required_repository.installation_complete: if not os.path.exists( required_repository_package_install_dir ): print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) repo_files_dir = required_repository.repo_files_directory( app ) @@ -156,22 +220,26 @@ required_repository_owner, required_repository_changeset_revision ) config_to_use = tmp_filename - tool_dependencies, actions_dict = populate_actions_dict( app=app, - dependent_install_dir=dependent_install_dir, - required_install_dir=required_repository_package_install_dir, - tool_shed_repository=tool_shed_repository, - required_repository=required_repository, - package_name=package_name, - package_version=package_version, - tool_dependencies_config=config_to_use ) + + tool_dependencies, package_env_sh_file = find_complex_dependency_package( + app=app, + dependent_install_dir=dependent_install_dir, + required_install_dir=required_repository_package_install_dir, + tool_shed_repository=tool_shed_repository, + required_repository=required_repository, + package_name=package_name, + package_version=package_version, + tool_dependencies_config=config_to_use + ) + if package_env_sh_file: + os.symlink( package_env_sh_file, os.path.join( dependent_install_dir, "env.sh" ) ) if tmp_filename: try: os.remove( tmp_filename ) except: pass for tool_dependency in tool_dependencies: - # Install and build the package via fabric and update the tool_dependency record accordingly.. - tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) + tool_dependency = __mark_tool_dependency_installed( app, tool_dependency) handled_tool_dependencies.append( tool_dependency ) else: message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ @@ -179,113 +247,6 @@ raise Exception( message ) return handled_tool_dependencies -def handle_set_environment_entry_for_package( app, install_dir, tool_shed_repository, package_name, package_version, elem, required_repository ): - """ - Populate a list of actions for creating an env.sh file for a dependent repository. The received elem is the <package> tag set associated - with the tool-dependencies.xml file for one of the received tool_shed_repository's repository dependency. - """ - action_dict = {} - actions = [] - tool_dependencies = [] - for package_elem in elem: - if package_elem.tag == 'install': - # Create the new tool_dependency record in the database. - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=package_name, - version=package_version, - type='package', - status=app.model.ToolDependency.installation_status.NEVER_INSTALLED, - set_status=True ) - # Get the installation method version from a tag like: <install version="1.0"> - package_install_version = package_elem.get( 'version', '1.0' ) - if package_install_version == '1.0': - # Update the tool dependency's status. - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLING ) - # Since the required tool dependency is installed for a repository dependency, we first need to inspect the <actions> tag set to find - # the <action type="set_environment"> tag. - env_var_dicts = [] - for actions_elem in package_elem: - for action_elem in actions_elem: - action_type = action_elem.get( 'type', 'shell_command' ) - if action_type == 'set_environment': - # <action type="set_environment"> - # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> - # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - # </action> - for env_elem in action_elem: - if env_elem.tag == 'environment_variable': - env_var_dict = td_common_util.create_env_var_dict( env_elem, tool_dependency_install_dir=install_dir ) - if env_var_dict: - if env_var_dict not in env_var_dicts: - env_var_dicts.append( env_var_dict ) - elif action_type == 'setup_virtualenv': - # Add the virtualenv's site-packages to PYTHONPATH and bin to PATH. This is a bit hackish. - site_packages_command = "%s -c 'import os, sys; print os.path.join(sys.prefix, \"lib\", \"python\" + sys.version[:3], \"site-packages\")'" % os.path.join( install_dir, "venv", "bin", "python" ) - output = fabric_util.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) - if output.return_code: - log.error( 'Tool dependency %s includes a setup_virtualenv action but venv python is broken: ' % \ - ( str( tool_dependency.name ), str( output.stderr ) ) ) - elif not os.path.exists( output.stdout ): - log.error( "virtualenv's site-packages directory '%s' does not exist", str( output.stdout ) ) - else: - env_var_dicts.append( dict( name="PYTHONPATH", action="prepend_to", value=output.stdout ) ) - env_var_dicts.append( dict( name="PATH", action="prepend_to", value=os.path.join( install_dir, 'venv', 'bin' ) ) ) - if env_var_dicts: - if required_repository.status in [ app.model.ToolShedRepository.installation_status.INSTALLED, - app.model.ToolShedRepository.installation_status.DEACTIVATED ]: - # Handle the case where we have an installed required repository due to the prior_installation_required = True - # setting in the received tool_shed_repository's tool_dependencies.xml file and the required repository's - # tool_dependencies.xml file may include the use of the $ENV[] variable inheritance feature. To handle this, - # we will replace the current "value" entries in each env_var_dict with the actual path taken from the env.sh - # file generated for the installed required repository. Each env_var_dict currently looks something like this: - # {'action': 'append_to', 'name': 'LD_LIBRARY_PATH', 'value': '$BOOST_ROOT_DIR/lib/'} - # We'll read the contents of the received required_repository's env.sh file and replace the 'value' entry of - # each env_var_dict with the associated value in the env.sh file. - new_env_var_dicts = [] - env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, - repository_name=required_repository.name, - repository_owner=required_repository.owner, - repository_changeset_revision=required_repository.installed_changeset_revision, - tool_dependency_type='package', - tool_dependency_name=package_name, - tool_dependency_version=package_version ) - env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) - if os.path.exists( env_sh_file_path ): - for i, line in enumerate( open( env_sh_file_path, 'r' ) ): - env_var_dict = env_var_dicts[ i ] - action = env_var_dict.get( 'action', None ) - name = env_var_dict.get( 'name', None ) - value = env_var_dict.get( 'value', None ) - if action and name and value: - new_value = parse_env_shell_entry( action, name, value, line ) - env_var_dict[ 'value' ] = new_value - new_env_var_dicts.append( env_var_dict ) - else: - error_message = 'Invalid file %s specified, ignoring set_environment_for_install action.' % str( env_sh_file_path ) - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, - tool_dependency, - error_message, - remove_installation_path=False ) - action_dict[ 'environment_variable' ] = new_env_var_dicts - else: - action_dict[ 'environment_variable' ] = env_var_dicts - actions.append( ( 'set_environment', action_dict ) ) - if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, - app.model.ToolDependency.installation_status.INSTALLED ]: - # Update the tool dependency's status. - tool_dependency = \ - tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLED ) - # Accumulate processed tool dependencies to return to the caller. - tool_dependencies.append( tool_dependency ) - else: - raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' ) - return tool_dependencies, actions - return tool_dependencies, actions def install_and_build_package_via_fabric( app, tool_dependency, actions_dict ): sa_session = app.model.context.current @@ -301,17 +262,10 @@ tool_dependency, error_message, remove_installation_path=False ) - if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, - app.model.ToolDependency.installation_status.INSTALLED ]: - log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ - ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) ) - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLED, - error_message=None, - remove_from_disk=False ) + tool_dependency = __mark_tool_dependency_installed( app, tool_dependency) return tool_dependency + def install_package( app, elem, tool_shed_repository, tool_dependencies=None ): # The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository. sa_session = app.model.context.current @@ -821,60 +775,22 @@ tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) return tool_dependency -def parse_env_shell_entry( action, name, value, line ): - new_value = value - var_name = '$%s' % name - tmp_value = line.split( '=' )[ 1 ] - if action == 'prepend_to': - # PATH=/test/package_rdkit_2012_12/62ebd7bb637a/rdkit/bin:$PATH; export PATH - new_value = tmp_value.split( ':%s' % var_name )[ 0 ] - elif action == 'set_to': - # RDBASE=test/package_rdkit_2012_12/62ebd7bb637a/rdkit; export RDBASE - new_value = tmp_value.split( ';' )[ 0 ] - elif action == 'append_to': - # LD_LIBRARY_PATH=$LD_LIBRARY_PATH:test/package_rdkit_2012_12/62ebd7bb637a/rdkit/lib/; export LD_LIBRARY_PATH - new_value = tmp_value.split( ':' )[ 1 ] - new_value = new_value.split( ';' )[ 0 ] - return new_value -def populate_actions_dict( app, dependent_install_dir, required_install_dir, tool_shed_repository, required_repository, package_name, package_version, tool_dependencies_config ): +# TODO: Move to tool_dependency_util? +def required_repository_package_env( app, package_name, package_version, required_repository ): """ - Populate an actions dictionary that can be sent to fabric_util.install_and_build_package. This method handles the scenario where a tool_dependencies.xml - file defines a complex repository dependency. In this case, the tool dependency package will be installed in a separate repository and the tool dependency - defined for the dependent repository will use an environment_variable setting defined in it's env.sh file to locate the required package. This method - basically does what the install_via_fabric method does, but restricts it's activity to the <action type="set_environment"> tag set within the required - repository's tool_dependencies.xml file. + Return path to env.sh file in required repository if the required repository has been installed. """ - sa_session = app.model.context.current - if not os.path.exists( dependent_install_dir ): - os.makedirs( dependent_install_dir ) - actions_dict = dict( install_dir=dependent_install_dir ) - if package_name: - actions_dict[ 'package_name' ] = package_name - tool_dependencies = [] - action_dict = {} - if tool_dependencies_config: - required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - if required_td_tree: - required_td_root = required_td_tree.getroot() - for required_td_elem in required_td_root: - # Find the appropriate package name and version. - if required_td_elem.tag == 'package': - # <package name="bwa" version="0.5.9"> - required_td_package_name = required_td_elem.get( 'name', None ) - required_td_package_version = required_td_elem.get( 'version', None ) - if required_td_package_name==package_name and required_td_package_version==package_version: - tool_dependencies, actions = handle_set_environment_entry_for_package( app=app, - install_dir=required_install_dir, - tool_shed_repository=tool_shed_repository, - package_name=package_name, - package_version=package_version, - elem=required_td_elem, - required_repository=required_repository ) - if actions: - actions_dict[ 'actions' ] = actions - break - return tool_dependencies, actions_dict + env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, + repository_name=required_repository.name, + repository_owner=required_repository.owner, + repository_changeset_revision=required_repository.installed_changeset_revision, + tool_dependency_type='package', + tool_dependency_name=package_name, + tool_dependency_version=package_version ) + env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) + return env_sh_file_path + def run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=None, **kwd ): """ @@ -1019,3 +935,17 @@ for arg in args: parts.append( arg.strip( '/' ) ) return '/'.join( parts ) + + +# TODO: Move to tool_dependency_util? +def __mark_tool_dependency_installed( app, tool_dependency ): + if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, + app.model.ToolDependency.installation_status.INSTALLED ]: + log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ + ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) ) + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLED, + error_message=None, + remove_from_disk=False ) + return tool_dependency diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -95,18 +95,25 @@ invalid_revisions = 0 records_checked = 0 # Do not check metadata records that have an entry in the skip_tool_tests table, since they won't be tested anyway. - skip_metadata_ids = select( [ app.model.SkipToolTest.table.c.repository_metadata_id ] ) + print '# -------------------------------------------------------------------------------------------' + print '# The skip_tool_test setting has been set for the following repository revision, so they will not be tested.' + skip_metadata_ids = [] + for skip_tool_test in app.sa_session.query( app.model.SkipToolTest ): + print '# repository_metadata_id: %s, changeset_revision: %s' % \ + ( str( skip_tool_test.repository_metadata_id ), str( skip_tool_test.initial_changeset_revision ) ) + print 'reason: %s' % str( skip_tool_test.comment ) + skip_metadata_ids.append( skip_tool_test.repository_metadata_id ) # Get the list of metadata records to check for functional tests and test data. Limit this to records that have not been flagged do_not_test, # since there's no need to check them again if they won't be tested anyway. Also filter out changeset revisions that are not downloadable, # because it's redundant to test a revision that a user can't install. for repository_metadata in app.sa_session.query( app.model.RepositoryMetadata ) \ .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, app.model.RepositoryMetadata.table.c.includes_tools == True, - app.model.RepositoryMetadata.table.c.do_not_test == False, - not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ): - # Clear any old invalid tests for this metadata revision, since this could lead to duplication of invalid test rows, - # or tests incorrectly labeled as invalid. + app.model.RepositoryMetadata.table.c.do_not_test == False ) ): + # Initialize some items. missing_test_components = [] + revision_has_test_data = False + testable_revision = False repository = repository_metadata.repository records_checked += 1 # Check the next repository revision. @@ -117,15 +124,14 @@ repository = repository_metadata.repository if repository.id not in checked_repository_ids: checked_repository_ids.append( repository.id ) - if verbosity >= 1: - print '# -------------------------------------------------------------------------------------------' - print '# Now checking revision %s of %s, owned by %s.' % ( changeset_revision, name, owner ) + print '# -------------------------------------------------------------------------------------------' + print '# Checking revision %s of %s owned by %s.' % ( changeset_revision, name, owner ) + if repository_metadata.id in skip_metadata_ids: + print'# Skipping revision %s of %s owned by %s because the skip_tool_test setting has been set.' % ( changeset_revision, name, owner ) # If this changeset revision has no tools, we don't need to do anything here, the install and test script has a filter for returning # only repositories that contain tools. tool_dicts = metadata.get( 'tools', None ) if tool_dicts is not None: - has_test_data = False - testable_revision = False # Clone the repository up to the changeset revision we're checking. repo_dir = repository.repo_path( app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -139,29 +145,30 @@ if '.hg' in dirs: dirs.remove( '.hg' ) if 'test-data' in dirs: - has_test_data = True + revision_has_test_data = True test_data_path = os.path.join( root, dirs[ dirs.index( 'test-data' ) ] ) break - if verbosity >= 1: - if has_test_data: - print '# Test data directory found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) - else: - print '# Test data directory missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) - print '# Checking for functional tests in changeset revision %s of %s, owned by %s.' % \ - ( changeset_revision, name, owner ) - # Inspect each tool_dict for defined functional tests. + if revision_has_test_data: + print '# Test data directory found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + else: + print '# Test data directory missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + print '# Checking for functional tests in changeset revision %s of %s, owned by %s.' % \ + ( changeset_revision, name, owner ) + # Inspect each tool_dict for defined functional tests. If there are no tests, this tool should not be tested, since the + # tool functional tests only report failure if the test itself fails, not if it's missing or undefined. Filtering out those + # repositories at this step will reduce the number of "false negatives" the automated functional test framework produces. for tool_dict in tool_dicts: + failure_reason = '' + problem_found = False + tool_has_defined_tests = False + tool_has_test_files = False + missing_test_files = [] tool_count += 1 tool_id = tool_dict[ 'id' ] tool_version = tool_dict[ 'version' ] tool_guid = tool_dict[ 'guid' ] - if verbosity >= 2: - print "# Checking tool ID '%s' in changeset revision %s of %s." % \ - ( tool_id, changeset_revision, name ) - # If there are no tests, this tool should not be tested, since the tool functional tests only report failure if the test itself fails, - # not if it's missing or undefined. Filtering out those repositories at this step will reduce the number of "false negatives" the - # automated functional test framework produces. - tool_has_tests = False + if verbosity >= 1: + print "# Checking tool ID '%s' in changeset revision %s of %s." % ( tool_id, changeset_revision, name ) defined_test_dicts = tool_dict.get( 'tests', None ) if defined_test_dicts is not None: # We need to inspect the <test> tags because the following tags... @@ -182,33 +189,26 @@ outputs = defined_test_dict.get( 'outputs', [] ) if inputs and outputs: # At least one tool within the repository has a valid <test> tag. - tool_has_tests = True + tool_has_defined_tests = True break - if tool_has_tests: - if verbosity >= 2: - print "# Tool ID '%s' in changeset revision %s of %s has one or more valid functional tests defined." % \ - ( tool_id, changeset_revision, name ) + if tool_has_defined_tests: + print "# Tool ID '%s' in changeset revision %s of %s has one or more valid functional tests defined." % \ + ( tool_id, changeset_revision, name ) has_tests += 1 else: - if verbosity >= 2: - print '# No functional tests defined for %s.' % tool_id + print '# No functional tests defined for %s.' % tool_id no_tests += 1 - failure_reason = '' - problem_found = False - missing_test_files = [] - has_test_files = False - if tool_has_tests and has_test_data: + if tool_has_defined_tests and revision_has_test_data: missing_test_files = check_for_missing_test_files( defined_test_dicts, test_data_path ) if missing_test_files: - if verbosity >= 2: - print "# Tool ID '%s' in changeset revision %s of %s is missing one or more required test files: %s" % \ - ( tool_id, changeset_revision, name, ', '.join( missing_test_files ) ) + print "# Tool id '%s' in changeset revision %s of %s is missing one or more required test files: %s" % \ + ( tool_id, changeset_revision, name, ', '.join( missing_test_files ) ) else: - has_test_files = True - if not has_test_data: + tool_has_test_files = True + if not revision_has_test_data: failure_reason += 'Repository does not have a test-data directory. ' problem_found = True - if not tool_has_tests: + if not tool_has_defined_tests: failure_reason += 'Functional test definitions missing for %s. ' % tool_id problem_found = True if missing_test_files: @@ -219,23 +219,22 @@ if problem_found: if test_errors not in missing_test_components: missing_test_components.append( test_errors ) - if tool_has_tests and has_test_files: + if tool_has_defined_tests and tool_has_test_files: + print '# Revision %s of %s owned by %s is a testable revision.' % ( changeset_revision, name, owner ) testable_revision = True # Remove the cloned repository path. This has to be done after the check for required test files, for obvious reasons. if os.path.exists( work_dir ): shutil.rmtree( work_dir ) if not missing_test_components: valid_revisions += 1 - if verbosity >= 1: - print '# All tools have functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + print '# All tools have functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) else: invalid_revisions += 1 + print '# Some tools have problematic functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) if verbosity >= 1: - print '# Some tools have problematic functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) - if verbosity >= 2: - for invalid_test in missing_test_components: - if 'missing_components' in invalid_test: - print '# %s' % invalid_test[ 'missing_components' ] + for missing_test_component in missing_test_components: + if 'missing_components' in missing_test_component: + print '# %s' % missing_test_component[ 'missing_components' ] if not info_only: # Get or create the list of tool_test_results dictionaries. if repository_metadata.tool_test_results is not None: @@ -249,8 +248,9 @@ # install_and_test_tool_sed_repositories.sh script which will further populate the tool_test_results_dict. tool_test_results_dict = tool_test_results_dicts[ 0 ] if len( tool_test_results_dict ) <= 1: - # We can re-use the mostly empty tool_test_results_dict for this run, but we need to eliminate it from - # the list of tool_test_results_dicts since it will be re-inserted later. + # We can re-use the mostly empty tool_test_results_dict for this run because it is either empty or it contains only + # a test_environment entry. If we use it we need to temporarily eliminate it from the list of tool_test_results_dicts + # since it will be re-inserted later. tool_test_results_dict = tool_test_results_dicts.pop( 0 ) else: # The latest tool_test_results_dict has been populated with the results of a test run, so it cannot be used. @@ -259,6 +259,11 @@ # Create a new dictionary for the most recent test run. tool_test_results_dict = {} test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) + # Add the current time as the approximate time that this test run occurs. A similar value will also be + # set to the repository_metadata.time_last_tested column, but we also store it here because the Tool Shed + # may be configured to store multiple test run results, so each must be associated with a time stamp. + now = time.strftime( "%Y-%m-%d %H:%M:%S" ) + test_environment_dict[ 'time_tested' ] = now test_environment_dict[ 'tool_shed_database_version' ] = get_database_version( app ) test_environment_dict[ 'tool_shed_mercurial_version' ] = __version__.version test_environment_dict[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) @@ -281,7 +286,13 @@ print "# and it is not the latest downloadable revision." repository_metadata.do_not_test = True repository_metadata.tools_functionally_correct = False - repository_metadata.missing_test_components = True + if not testable_revision: + # Even though some tools may be missing test components, it may be possible to test other tools. Since the + # install and test framework filters out repositories marked as missing test components, we'll set it only if + # no tools can be tested. + print '# Setting missing_test_components to True for revision %s of %s owned by %s because all tools are missing test components.' % \ + ( changeset_revision, name, owner ) + repository_metadata.missing_test_components = True tool_test_results_dict[ 'missing_test_components' ] = missing_test_components # Store only the configured number of test runs. num_tool_test_results_saved = int( app.config.num_tool_test_results_saved ) diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1052,45 +1052,51 @@ """Return a folder hierarchy containing tool dependencies.""" # This container is displayed only in the tool shed. if tool_test_results_dicts: - multiple_tool_test_results_dicts = len( tool_test_results_dicts ) > 1 test_results_dict_id = 0 folder_id += 1 tool_test_results_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) + multiple_tool_test_results_dicts = len( tool_test_results_dicts ) > 1 + if multiple_tool_test_results_dicts: + folder_id += 1 + test_runs_folder = Folder( id=folder_id, key='test_runs', label='Test runs', parent=tool_test_results_root_folder ) + tool_test_results_root_folder.folders.append( test_runs_folder ) for index, tool_test_results_dict in enumerate( tool_test_results_dicts ): test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) - if test_environment_dict is not None: - time_tested = test_environment_dict.get( 'time_tested', 'unknown_%d' % index ) - if multiple_tool_test_results_dicts: - folder_id += 1 - containing_folder = Folder( id=folder_id, key='test_results', label=time_tested, parent=tool_test_results_root_folder ) - else: - containing_folder = tool_test_results_root_folder - test_results_dict_id += 1 - #folder_id += 1 - #test_results_folder = Folder( id=folder_id, key='test_results', label='Automated test environment', parent=containing_folder ) - #containing_folder.folders.append( test_results_folder ) + if test_environment_dict is None: + # the test environment entry will exist only if the preparation script check_re;ositories_for_functional_tests.py + # was executed prior to the ~/install_and_test_repositories/functional_tests.py script. If that did not occur, + # we'll display test result, but the test_environment entries will not be complete. + test_environment_dict = {} + time_tested = test_environment_dict.get( 'time_tested', 'unknown_%d' % index ) + if multiple_tool_test_results_dicts: folder_id += 1 - folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) - containing_folder.folders.append( folder ) - architecture = test_environment_dict.get( 'architecture', '' ) - galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' ) - galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' ) - python_version = test_environment_dict.get( 'python_version', '' ) - system = test_environment_dict.get( 'system', '' ) - tool_shed_database_version = test_environment_dict.get( 'tool_shed_database_version', '' ) - tool_shed_mercurial_version = test_environment_dict.get( 'tool_shed_mercurial_version', '' ) - tool_shed_revision = test_environment_dict.get( 'tool_shed_revision', '' ) - test_environment = TestEnvironment( id=1, - architecture=architecture, - galaxy_database_version=galaxy_database_version, - galaxy_revision=galaxy_revision, - python_version=python_version, - system=system, - time_tested=time_tested, - tool_shed_database_version=tool_shed_database_version, - tool_shed_mercurial_version=tool_shed_mercurial_version, - tool_shed_revision=tool_shed_revision ) - folder.test_environments.append( test_environment ) + containing_folder = Folder( id=folder_id, key='test_results', label=time_tested, parent=test_runs_folder ) + test_runs_folder.folders.append( containing_folder ) + else: + containing_folder = tool_test_results_root_folder + test_results_dict_id += 1 + folder_id += 1 + folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) + containing_folder.folders.append( folder ) + architecture = test_environment_dict.get( 'architecture', '' ) + galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' ) + galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' ) + python_version = test_environment_dict.get( 'python_version', '' ) + system = test_environment_dict.get( 'system', '' ) + tool_shed_database_version = test_environment_dict.get( 'tool_shed_database_version', '' ) + tool_shed_mercurial_version = test_environment_dict.get( 'tool_shed_mercurial_version', '' ) + tool_shed_revision = test_environment_dict.get( 'tool_shed_revision', '' ) + test_environment = TestEnvironment( id=1, + architecture=architecture, + galaxy_database_version=galaxy_database_version, + galaxy_revision=galaxy_revision, + python_version=python_version, + system=system, + time_tested=time_tested, + tool_shed_database_version=tool_shed_database_version, + tool_shed_mercurial_version=tool_shed_mercurial_version, + tool_shed_revision=tool_shed_revision ) + folder.test_environments.append( test_environment ) not_tested_dict = tool_test_results_dict.get( 'not_tested', {} ) if not_tested_dict: folder_id += 1 @@ -1120,6 +1126,9 @@ containing_folder.folders.append( folder ) failed_test_id = 0 for failed_tests_dict in failed_tests_dicts: + # TODO: Remove this when invalid test data is eliminated. + if isinstance( failed_tests_dict, list ): + failed_tests_dict = failed_tests_dict[ 0 ] failed_test_id += 1 failed_test = FailedTest( id=failed_test_id, stderr=failed_tests_dict.get( 'stderr', '' ), @@ -1153,6 +1162,7 @@ key='installation_errors', label='Installation errors', parent=containing_folder ) + containing_folder.installation_errors.append( installation_error_base_folder ) if current_repository_errors: folder_id += 1 subfolder = Folder( id=folder_id, @@ -1203,10 +1213,6 @@ error_message=tool_dependency_error_dict.get( 'error_message', '' ) ) subfolder.tool_dependency_installation_errors.append( tool_dependency_installation_error ) installation_error_base_folder.folders.append( subfolder ) - containing_folder.installation_errors.append( installation_error_base_folder ) - #containing_folder.folders.append( containing_folder ) - if multiple_tool_test_results_dicts: - tool_test_results_root_folder.folders.append( containing_folder ) else: tool_test_results_root_folder = None return folder_id, tool_test_results_root_folder diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -363,6 +363,8 @@ """ error_message = '' latest_revision_only = '-check_all_revisions' not in sys.argv + if latest_revision_only: + log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' ) repository_dicts = [] params = urllib.urlencode( dict( do_not_test='false', downloadable='true', @@ -374,13 +376,12 @@ baseline_repository_dicts, error_message = json_from_url( api_url ) if error_message: return None, error_message - log.debug( 'The Tool Shed API returned %d metadata revisions for installation and testing.' % len( baseline_repository_dicts ) ) for baseline_repository_dict in baseline_repository_dicts: # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the # module that will generate the install methods. repository_dict, error_message = get_repository_dict( galaxy_tool_shed_url, baseline_repository_dict ) if error_message: - log.debug( 'Error getting additional details about repository %s from the API: %s' % ( str( name ), error_message ) ) + log.debug( 'Error getting additional details from the API: %s' % str( error_message ) ) else: # Don't test empty repositories. changeset_revision = baseline_repository_dict[ 'changeset_revision' ] @@ -393,10 +394,6 @@ repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) else: repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - if latest_revision_only: - skipped_previous = ' and metadata revisions that are not the most recent' - else: - skipped_previous = '' if testing_single_repository: tsr_name = testing_single_repository[ 'name' ] tsr_owner = testing_single_repository[ 'owner' ] @@ -414,14 +411,15 @@ return repository_dicts, error_message return repository_dicts, error_message # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable. - log.debug( "Retrieved %d repositories from the API url: %s." % ( len( repository_dicts ), str( galaxy_tool_shed_url ) ) ) - if '-list_repositories' in sys.argv: - log.debug( "Repositories for testing:" ) - for repository_dict in repository_dicts: - log.debug( "Revision %s of repository %s owned by %s" % \ - ( str( repository_dict.get( 'changeset_revision', None ) ), \ - str( repository_dict.get( 'name', None ) ), \ - str( repository_dict.get( 'owner', None ) ) ) ) + log.debug( "The Tool Shed's API url...\n%s" % str( api_url ) ) + log.debug( "...retrieved %d repository revisions for testing." % len( repository_dicts ) ) + #if '-list_repositories' in sys.argv: + log.debug( "Repository revisions for testing:" ) + for repository_dict in repository_dicts: + log.debug( "Revision %s of repository %s owned by %s" % \ + ( str( repository_dict.get( 'changeset_revision', None ) ), \ + str( repository_dict.get( 'name', None ) ), \ + str( repository_dict.get( 'owner', None ) ) ) ) return repository_dicts, error_message def get_static_settings(): @@ -503,7 +501,7 @@ params = dict( tools_functionally_correct=False, do_not_test=False, test_install_error=True ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) # Since this repository is missing components, we do not want to test it, so deactivate it or uninstall it. # The deactivate flag is set to True if the environment variable GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES @@ -618,33 +616,39 @@ name = str( repository_dict[ 'name' ] ) owner = str( repository_dict[ 'owner' ] ) changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + log.debug( "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) ) # Populate the tool_test_results_dict. tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, encoded_repository_metadata_id ) - # The preparation script ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered - # information in the 'test_environment' and possibly the 'missing_test_components' entries of the first - # tool_test_results_dict in the list of tool_test_results_dicts. We need to be careful to not lose this - # information. - tool_test_results_dict = tool_test_results_dicts.pop( 0 ) - # See if this repository should be skipped for any reason. - skip_this_repository = False - skip_reason = None - for exclude_dict in exclude_list: - reason = exclude_dict[ 'reason' ] - exclude_repositories = exclude_dict[ 'repositories' ] - if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: - skip_this_repository = True - skip_reason = reason - break - if skip_this_repository: - tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) - params = dict( tools_functionally_correct=False, - do_not_test=False ) - # TODO: do something usefule with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) - log.debug( "Not testing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) + if error_message: + log.debug( error_message ) else: - if error_message: - log.debug( error_message ) + # The preparation script ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered + # information in the 'test_environment' and possibly the 'missing_test_components' entries of the first + # tool_test_results_dict in the list of tool_test_results_dicts. We need to be careful to not lose this + # information. + try: + tool_test_results_dict = tool_test_results_dicts.pop( 0 ) + except Exception, e: + log.exception( "Invalid list of tool_test_results_dicts %s: %s" % ( str( tool_test_results_dicts ), str( e ) ) ) + continue + # See if this repository should be skipped for any reason. + this_repository_is_in_the_exclude_lost = False + skip_reason = None + for exclude_dict in exclude_list: + reason = exclude_dict[ 'reason' ] + exclude_repositories = exclude_dict[ 'repositories' ] + if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: + this_repository_is_in_the_exclude_lost = True + skip_reason = reason + break + if this_repository_is_in_the_exclude_lost: + tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) + params = dict( tools_functionally_correct=False, + do_not_test=False ) + # TODO: do something useful with response_dict + response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) + log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \ + ( changeset_revision, name, owner ) ) else: test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) test_environment_dict = get_test_environment( test_environment_dict ) @@ -678,7 +682,7 @@ params = dict( tools_functionally_correct=False, test_install_error=True, do_not_test=False ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) try: if deactivate: @@ -736,7 +740,7 @@ params = dict( tools_functionally_correct=False, do_not_test=False, test_install_error=False ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, @@ -1066,13 +1070,14 @@ exclude_count += 1 exclude_dict[ 'repositories' ].append( repository_tuple ) exclude_list.append( exclude_dict ) - log.debug( '%s repositories will be excluded from testing...' % str( exclude_count ) ) - if '-list_repositories' in sys.argv: - for name, owner, changeset_revision in exclude_verbose: - if changeset_revision: - log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) ) - else: - log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) + log.debug( 'The xml document %s containing the exclude list defines the following %s repositories to be excluded from testing...' % \ + ( str( xml_filename ), str( exclude_count ) ) ) + #if '-list_repositories' in sys.argv: + for name, owner, changeset_revision in exclude_verbose: + if changeset_revision: + log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) ) + else: + log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) return exclude_list def register_test_result( url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ): @@ -1202,17 +1207,18 @@ params = dict( tools_functionally_correct=True, do_not_test=False, test_install_error=False ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( str( changeset_revision ), str( name ) ) ) else: - tool_test_results_dict[ 'failed_tests' ].append( extract_log_data( result, from_tool_test=True ) ) + # The extract_log_data() netod returns a list. + tool_test_results_dict[ 'failed_tests' ] = extract_log_data( result, from_tool_test=True ) results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_dict ) params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed successfully but did not pass functional tests.' % \ ( str( changeset_revision ), str( name ) ) ) diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -280,8 +280,6 @@ <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-rna-tools" name="NGS: RNA Analysis"><label id="rna_seq" text="RNA-seq" /> diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -340,8 +340,6 @@ <tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_indexer.py --- a/tools/genetrack/genetrack_indexer.py +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. - -usage: %prog input output shift -""" - -import sys, shutil, os -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import tabs2genetrack -from genetrack import logger - -if __name__ == "__main__": - import os - os.environ[ 'LC_ALL' ] = 'C' - #os.system( 'export' ) - - parser = tabs2genetrack.option_parser() - - options, args = parser.parse_args() - - # uppercase the format - options.format = options.format.upper() - - if options.format not in ('BED', 'GFF'): - sys.stdout = sys.stderr - parser.print_help() - sys.exit(-1) - - logger.disable(options.verbosity) - - # missing file names - if not (options.inpname and options.outname and options.format): - parser.print_help() - sys.exit(-1) - else: - tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ - format=options.format, shift=options.shift, index=options.index, options=options) diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_indexer.xml --- a/tools/genetrack/genetrack_indexer.xml +++ /dev/null @@ -1,64 +0,0 @@ -<tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1"> - - <description>on a BED file</description> - - <command interpreter="python"> - genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x - </command> - - <inputs> - - <param format="bed6" name="input" type="data" help="Input data"> - <label>Select input bed file</label> - </param> - - <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> - <label>Shift at 5' end</label> - </param> - -  - - </inputs> - - <outputs> - <data format="genetrack" name="output" /> - </outputs> - -<help> -**Help** - -This tool will create a visualization of the bed file that is selected. - -**Parameters** - -- **Shift at 5' end** should be used when the location of interest is at a fixed distance from - the 5' end for **all sequenced fragments**! - - For example if the sequenced sample consists - mono-nucleosomal DNA (146bp) we should expect that - each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. - Therefore we would enter 73 as the shift parameter. Once corrected the reads - on each strand will coincide and indicate the actual midpoints - of the nucleosomes. - - When shifting the averaging process in GeneTrack is able correct for longer or shorter - than expected fragment sizes as long as the errors are reasonably random. - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_peak_prediction.py --- a/tools/genetrack/genetrack_peak_prediction.py +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. - -usage: %prog input output level sigma mode exclusion strand -""" - -import sys -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import peakpred -from genetrack import logger - -if __name__ == "__main__": - - parser = peakpred.option_parser() - - options, args = parser.parse_args() - - logger.disable(options.verbosity) - - from genetrack import conf - - # trigger test mode - if options.test: - options.inpname = conf.testdata('test-hdflib-input.gtrack') - options.outname = conf.testdata('predictions.bed') - - # missing input file name - if not options.inpname and not options.outname: - parser.print_help() - else: - print 'Sigma = %s' % options.sigma - print 'Minimum peak = %s' % options.level - print 'Peak-to-peak = %s' % options.exclude - - peakpred.predict(options.inpname, options.outname, options) diff -r c2d705f7b50a51a9a3e8153da634ea61e9c3fec7 -r 9a5a8d18cd16ed3331ba996de21ed4d4dfa93da9 tools/genetrack/genetrack_peak_prediction.xml --- a/tools/genetrack/genetrack_peak_prediction.xml +++ /dev/null @@ -1,69 +0,0 @@ -<tool id="predict2genetrack" name="Peak predictor"> - - <description>on GeneTrack index</description> - - <command interpreter="python"> - genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x - </command> - - <inputs> - - <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/> - - <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values"> - <option value="gauss">Gaussian kernel</option> -  - </param> - - <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" /> - - - <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> - <option value="nolap">Maximal non-overlapping</option> -  - <option value="all">All peaks</option> - </param> - - <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance"> - </param> - - <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" /> - - <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately"> - <option value="all">Merge strands</option> -  - <option value="two">Separate strands</option> - </param> - - </inputs> - - <outputs> - <data format="bed" name="output" /> - </outputs> - -<help> -**Help** - -This tool will generate genome wide peak prediction from an index file. - -**Parameters** - -- **Smoothing method** the function used to average nearby values - -- **Smoothing value** the factor used in the method - -- **Prediction method** the function used to average nearby values - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 30 Nov '13

30 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/63006e23bf7d/ Changeset: 63006e23bf7d Branch: stable User: natefoo Date: 2013-11-30 18:46:53 Summary: Remove broken GeneTrack tools. Affected #: 6 files diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -284,8 +284,6 @@ <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-rna-tools" name="NGS: RNA Analysis"><label id="rna_seq" text="RNA-seq" /> diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -345,8 +345,6 @@ <tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_indexer.py --- a/tools/genetrack/genetrack_indexer.py +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. - -usage: %prog input output shift -""" - -import sys, shutil, os -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import tabs2genetrack -from genetrack import logger - -if __name__ == "__main__": - import os - os.environ[ 'LC_ALL' ] = 'C' - #os.system( 'export' ) - - parser = tabs2genetrack.option_parser() - - options, args = parser.parse_args() - - # uppercase the format - options.format = options.format.upper() - - if options.format not in ('BED', 'GFF'): - sys.stdout = sys.stderr - parser.print_help() - sys.exit(-1) - - logger.disable(options.verbosity) - - # missing file names - if not (options.inpname and options.outname and options.format): - parser.print_help() - sys.exit(-1) - else: - tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ - format=options.format, shift=options.shift, index=options.index, options=options) diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_indexer.xml --- a/tools/genetrack/genetrack_indexer.xml +++ /dev/null @@ -1,64 +0,0 @@ -<tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1"> - - <description>on a BED file</description> - - <command interpreter="python"> - genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x - </command> - - <inputs> - - <param format="bed6" name="input" type="data" help="Input data"> - <label>Select input bed file</label> - </param> - - <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> - <label>Shift at 5' end</label> - </param> - -  - - </inputs> - - <outputs> - <data format="genetrack" name="output" /> - </outputs> - -<help> -**Help** - -This tool will create a visualization of the bed file that is selected. - -**Parameters** - -- **Shift at 5' end** should be used when the location of interest is at a fixed distance from - the 5' end for **all sequenced fragments**! - - For example if the sequenced sample consists - mono-nucleosomal DNA (146bp) we should expect that - each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. - Therefore we would enter 73 as the shift parameter. Once corrected the reads - on each strand will coincide and indicate the actual midpoints - of the nucleosomes. - - When shifting the averaging process in GeneTrack is able correct for longer or shorter - than expected fragment sizes as long as the errors are reasonably random. - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_peak_prediction.py --- a/tools/genetrack/genetrack_peak_prediction.py +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. - -usage: %prog input output level sigma mode exclusion strand -""" - -import sys -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import peakpred -from genetrack import logger - -if __name__ == "__main__": - - parser = peakpred.option_parser() - - options, args = parser.parse_args() - - logger.disable(options.verbosity) - - from genetrack import conf - - # trigger test mode - if options.test: - options.inpname = conf.testdata('test-hdflib-input.gtrack') - options.outname = conf.testdata('predictions.bed') - - # missing input file name - if not options.inpname and not options.outname: - parser.print_help() - else: - print 'Sigma = %s' % options.sigma - print 'Minimum peak = %s' % options.level - print 'Peak-to-peak = %s' % options.exclude - - peakpred.predict(options.inpname, options.outname, options) diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_peak_prediction.xml --- a/tools/genetrack/genetrack_peak_prediction.xml +++ /dev/null @@ -1,69 +0,0 @@ -<tool id="predict2genetrack" name="Peak predictor"> - - <description>on GeneTrack index</description> - - <command interpreter="python"> - genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x - </command> - - <inputs> - - <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/> - - <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values"> - <option value="gauss">Gaussian kernel</option> -  - </param> - - <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" /> - - - <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> - <option value="nolap">Maximal non-overlapping</option> -  - <option value="all">All peaks</option> - </param> - - <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance"> - </param> - - <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" /> - - <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately"> - <option value="all">Merge strands</option> -  - <option value="two">Separate strands</option> - </param> - - </inputs> - - <outputs> - <data format="bed" name="output" /> - </outputs> - -<help> -**Help** - -This tool will generate genome wide peak prediction from an index file. - -**Parameters** - -- **Smoothing method** the function used to average nearby values - -- **Smoothing value** the factor used in the method - -- **Prediction method** the function used to average nearby values - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> https://bitbucket.org/galaxy/galaxy-central/commits/a508799de645/ Changeset: a508799de645 User: natefoo Date: 2013-11-30 18:47:19 Summary: merge stable. Affected #: 6 files diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -280,8 +280,6 @@ <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-rna-tools" name="NGS: RNA Analysis"><label id="rna_seq" text="RNA-seq" /> diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -340,8 +340,6 @@ <tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_indexer.py --- a/tools/genetrack/genetrack_indexer.py +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. - -usage: %prog input output shift -""" - -import sys, shutil, os -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import tabs2genetrack -from genetrack import logger - -if __name__ == "__main__": - import os - os.environ[ 'LC_ALL' ] = 'C' - #os.system( 'export' ) - - parser = tabs2genetrack.option_parser() - - options, args = parser.parse_args() - - # uppercase the format - options.format = options.format.upper() - - if options.format not in ('BED', 'GFF'): - sys.stdout = sys.stderr - parser.print_help() - sys.exit(-1) - - logger.disable(options.verbosity) - - # missing file names - if not (options.inpname and options.outname and options.format): - parser.print_help() - sys.exit(-1) - else: - tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ - format=options.format, shift=options.shift, index=options.index, options=options) diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_indexer.xml --- a/tools/genetrack/genetrack_indexer.xml +++ /dev/null @@ -1,64 +0,0 @@ -<tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1"> - - <description>on a BED file</description> - - <command interpreter="python"> - genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x - </command> - - <inputs> - - <param format="bed6" name="input" type="data" help="Input data"> - <label>Select input bed file</label> - </param> - - <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> - <label>Shift at 5' end</label> - </param> - -  - - </inputs> - - <outputs> - <data format="genetrack" name="output" /> - </outputs> - -<help> -**Help** - -This tool will create a visualization of the bed file that is selected. - -**Parameters** - -- **Shift at 5' end** should be used when the location of interest is at a fixed distance from - the 5' end for **all sequenced fragments**! - - For example if the sequenced sample consists - mono-nucleosomal DNA (146bp) we should expect that - each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. - Therefore we would enter 73 as the shift parameter. Once corrected the reads - on each strand will coincide and indicate the actual midpoints - of the nucleosomes. - - When shifting the averaging process in GeneTrack is able correct for longer or shorter - than expected fragment sizes as long as the errors are reasonably random. - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_peak_prediction.py --- a/tools/genetrack/genetrack_peak_prediction.py +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. - -usage: %prog input output level sigma mode exclusion strand -""" - -import sys -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import peakpred -from genetrack import logger - -if __name__ == "__main__": - - parser = peakpred.option_parser() - - options, args = parser.parse_args() - - logger.disable(options.verbosity) - - from genetrack import conf - - # trigger test mode - if options.test: - options.inpname = conf.testdata('test-hdflib-input.gtrack') - options.outname = conf.testdata('predictions.bed') - - # missing input file name - if not options.inpname and not options.outname: - parser.print_help() - else: - print 'Sigma = %s' % options.sigma - print 'Minimum peak = %s' % options.level - print 'Peak-to-peak = %s' % options.exclude - - peakpred.predict(options.inpname, options.outname, options) diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_peak_prediction.xml --- a/tools/genetrack/genetrack_peak_prediction.xml +++ /dev/null @@ -1,69 +0,0 @@ -<tool id="predict2genetrack" name="Peak predictor"> - - <description>on GeneTrack index</description> - - <command interpreter="python"> - genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x - </command> - - <inputs> - - <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/> - - <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values"> - <option value="gauss">Gaussian kernel</option> -  - </param> - - <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" /> - - - <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> - <option value="nolap">Maximal non-overlapping</option> -  - <option value="all">All peaks</option> - </param> - - <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance"> - </param> - - <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" /> - - <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately"> - <option value="all">Merge strands</option> -  - <option value="two">Separate strands</option> - </param> - - </inputs> - - <outputs> - <data format="bed" name="output" /> - </outputs> - -<help> -**Help** - -This tool will generate genome wide peak prediction from an index file. - -**Parameters** - -- **Smoothing method** the function used to average nearby values - -- **Smoothing value** the factor used in the method - -- **Prediction method** the function used to average nearby values - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 30 Nov '13

30 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3b6cdcd97595/ Changeset: 3b6cdcd97595 Branch: stable User: jmchilton Date: 2013-11-30 15:28:38 Summary: Fix from Jim Johnson for optional input handling in provenance API. Affected #: 1 file diff -r 51b4282dce3a411d02b982d1cca137884d5f6c2b -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -54,6 +54,8 @@ for p in job.parameters: out[p.name] = p.value for in_d in job.input_datasets: + if not in_d.dataset: + continue if follow: out[in_d.name] = self._get_record(trans, in_d.dataset, follow) else: https://bitbucket.org/galaxy/galaxy-central/commits/2b5329b6fba3/ Changeset: 2b5329b6fba3 User: jmchilton Date: 2013-11-30 15:29:06 Summary: Merge latest stable. Affected #: 1 file diff -r 228156daa575892f92d81c30a7e0f0ec4fa6b960 -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -58,6 +58,8 @@ for p in job.parameters: out[p.name] = p.value for in_d in job.input_datasets: + if not in_d.dataset: + continue if follow: out[in_d.name] = self._get_record(trans, in_d.dataset, follow) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Tool shed api fix for filtering tools that should not be tested via the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 29 Nov '13

29 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/228156daa575/ Changeset: 228156daa575 User: greg Date: 2013-11-29 23:06:02 Summary: Tool shed api fix for filtering tools that should not be tested via the tool shed's install and test framework. Affected #: 1 file diff -r 820ff73e8aab805b7f4f4f50cb66d0f47adc5bc2 -r 228156daa575892f92d81c30a7e0f0ec4fa6b960 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -107,10 +107,9 @@ skip_tool_test = kwd.get( 'skip_tool_test', None ) if skip_tool_test is not None: skip_tool_test = util.string_as_bool( skip_tool_test ) + if skip_tool_test: skipped_metadata_ids_subquery = select( [ trans.app.model.SkipToolTest.table.c.repository_metadata_id ] ) - if skip_tool_test: - clause_list.append( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) ) - else: + if skipped_metadata_ids_subquery: clause_list.append( not_( trans.model.RepositoryMetadata.id.in_( skipped_metadata_ids_subquery ) ) ) # Generate and execute the query. try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Attempt to display the results of the tool shed's install and test framework test run even if the preparation script was not executed before the test run.
by commits-noreply＠bitbucket.org 29 Nov '13

29 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/820ff73e8aab/ Changeset: 820ff73e8aab User: greg Date: 2013-11-29 22:28:25 Summary: Attempt to display the results of the tool shed's install and test framework test run even if the preparation script was not executed before the test run. Affected #: 1 file diff -r 8544d14f89dd48d313384a22117f56fa07a99974 -r 820ff73e8aab805b7f4f4f50cb66d0f47adc5bc2 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1062,37 +1062,41 @@ tool_test_results_root_folder.folders.append( test_runs_folder ) for index, tool_test_results_dict in enumerate( tool_test_results_dicts ): test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) - if test_environment_dict is not None: - time_tested = test_environment_dict.get( 'time_tested', 'unknown_%d' % index ) - if multiple_tool_test_results_dicts: - folder_id += 1 - containing_folder = Folder( id=folder_id, key='test_results', label=time_tested, parent=test_runs_folder ) - test_runs_folder.folders.append( containing_folder ) - else: - containing_folder = tool_test_results_root_folder - test_results_dict_id += 1 + if test_environment_dict is None: + # the test environment entry will exist only if the preparation script check_re;ositories_for_functional_tests.py + # was executed prior to the ~/install_and_test_repositories/functional_tests.py script. If that did not occur, + # we'll display test result, but the test_environment entries will not be complete. + test_environment_dict = {} + time_tested = test_environment_dict.get( 'time_tested', 'unknown_%d' % index ) + if multiple_tool_test_results_dicts: folder_id += 1 - folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) - containing_folder.folders.append( folder ) - architecture = test_environment_dict.get( 'architecture', '' ) - galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' ) - galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' ) - python_version = test_environment_dict.get( 'python_version', '' ) - system = test_environment_dict.get( 'system', '' ) - tool_shed_database_version = test_environment_dict.get( 'tool_shed_database_version', '' ) - tool_shed_mercurial_version = test_environment_dict.get( 'tool_shed_mercurial_version', '' ) - tool_shed_revision = test_environment_dict.get( 'tool_shed_revision', '' ) - test_environment = TestEnvironment( id=1, - architecture=architecture, - galaxy_database_version=galaxy_database_version, - galaxy_revision=galaxy_revision, - python_version=python_version, - system=system, - time_tested=time_tested, - tool_shed_database_version=tool_shed_database_version, - tool_shed_mercurial_version=tool_shed_mercurial_version, - tool_shed_revision=tool_shed_revision ) - folder.test_environments.append( test_environment ) + containing_folder = Folder( id=folder_id, key='test_results', label=time_tested, parent=test_runs_folder ) + test_runs_folder.folders.append( containing_folder ) + else: + containing_folder = tool_test_results_root_folder + test_results_dict_id += 1 + folder_id += 1 + folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) + containing_folder.folders.append( folder ) + architecture = test_environment_dict.get( 'architecture', '' ) + galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' ) + galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' ) + python_version = test_environment_dict.get( 'python_version', '' ) + system = test_environment_dict.get( 'system', '' ) + tool_shed_database_version = test_environment_dict.get( 'tool_shed_database_version', '' ) + tool_shed_mercurial_version = test_environment_dict.get( 'tool_shed_mercurial_version', '' ) + tool_shed_revision = test_environment_dict.get( 'tool_shed_revision', '' ) + test_environment = TestEnvironment( id=1, + architecture=architecture, + galaxy_database_version=galaxy_database_version, + galaxy_revision=galaxy_revision, + python_version=python_version, + system=system, + time_tested=time_tested, + tool_shed_database_version=tool_shed_database_version, + tool_shed_mercurial_version=tool_shed_mercurial_version, + tool_shed_revision=tool_shed_revision ) + folder.test_environments.append( test_environment ) not_tested_dict = tool_test_results_dict.get( 'not_tested', {} ) if not_tested_dict: folder_id += 1 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Minor fix for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 29 Nov '13

29 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8544d14f89dd/ Changeset: 8544d14f89dd User: greg Date: 2013-11-29 21:18:22 Summary: Minor fix for the tool shed's install and test framework. Affected #: 1 file diff -r 024e7ca6c1a6023d49f4f63014185d14760faecf -r 8544d14f89dd48d313384a22117f56fa07a99974 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -1070,7 +1070,7 @@ exclude_count += 1 exclude_dict[ 'repositories' ].append( repository_tuple ) exclude_list.append( exclude_dict ) - log.debug( 'The xml document %s containing the exclude list %s defines the following %s repositories to be excluded from testing...' % \ + log.debug( 'The xml document %s containing the exclude list defines the following %s repositories to be excluded from testing...' % \ ( str( xml_filename ), str( exclude_count ) ) ) #if '-list_repositories' in sys.argv: for name, owner, changeset_revision in exclude_verbose: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Additional code cleanup, better logging and more minor fixes for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 29 Nov '13

29 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/024e7ca6c1a6/ Changeset: 024e7ca6c1a6 User: greg Date: 2013-11-29 20:34:35 Summary: Additional code cleanup, better logging and more minor fixes for the tool shed's install and test framework. Affected #: 2 files diff -r 864f8f4c466e4c031739549ea6a038dd70a4ed9a -r 024e7ca6c1a6023d49f4f63014185d14760faecf lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -95,17 +95,25 @@ invalid_revisions = 0 records_checked = 0 # Do not check metadata records that have an entry in the skip_tool_tests table, since they won't be tested anyway. - skip_metadata_ids = select( [ app.model.SkipToolTest.table.c.repository_metadata_id ] ) + print '# -------------------------------------------------------------------------------------------' + print '# The skip_tool_test setting has been set for the following repository revision, so they will not be tested.' + skip_metadata_ids = [] + for skip_tool_test in app.sa_session.query( app.model.SkipToolTest ): + print '# repository_metadata_id: %s, changeset_revision: %s' % \ + ( str( skip_tool_test.repository_metadata_id ), str( skip_tool_test.initial_changeset_revision ) ) + print 'reason: %s' % str( skip_tool_test.comment ) + skip_metadata_ids.append( skip_tool_test.repository_metadata_id ) # Get the list of metadata records to check for functional tests and test data. Limit this to records that have not been flagged do_not_test, # since there's no need to check them again if they won't be tested anyway. Also filter out changeset revisions that are not downloadable, # because it's redundant to test a revision that a user can't install. for repository_metadata in app.sa_session.query( app.model.RepositoryMetadata ) \ .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, app.model.RepositoryMetadata.table.c.includes_tools == True, - app.model.RepositoryMetadata.table.c.do_not_test == False, - not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ): + app.model.RepositoryMetadata.table.c.do_not_test == False ) ): # Initialize some items. missing_test_components = [] + revision_has_test_data = False + testable_revision = False repository = repository_metadata.repository records_checked += 1 # Check the next repository revision. @@ -117,13 +125,13 @@ if repository.id not in checked_repository_ids: checked_repository_ids.append( repository.id ) print '# -------------------------------------------------------------------------------------------' - print '# Now checking revision %s of %s, owned by %s.' % ( changeset_revision, name, owner ) + print '# Checking revision %s of %s owned by %s.' % ( changeset_revision, name, owner ) + if repository_metadata.id in skip_metadata_ids: + print'# Skipping revision %s of %s owned by %s because the skip_tool_test setting has been set.' % ( changeset_revision, name, owner ) # If this changeset revision has no tools, we don't need to do anything here, the install and test script has a filter for returning # only repositories that contain tools. tool_dicts = metadata.get( 'tools', None ) if tool_dicts is not None: - has_test_data = False - testable_revision = False # Clone the repository up to the changeset revision we're checking. repo_dir = repository.repo_path( app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -137,27 +145,30 @@ if '.hg' in dirs: dirs.remove( '.hg' ) if 'test-data' in dirs: - has_test_data = True + revision_has_test_data = True test_data_path = os.path.join( root, dirs[ dirs.index( 'test-data' ) ] ) break - if has_test_data: + if revision_has_test_data: print '# Test data directory found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) else: print '# Test data directory missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) print '# Checking for functional tests in changeset revision %s of %s, owned by %s.' % \ ( changeset_revision, name, owner ) - # Inspect each tool_dict for defined functional tests. + # Inspect each tool_dict for defined functional tests. If there are no tests, this tool should not be tested, since the + # tool functional tests only report failure if the test itself fails, not if it's missing or undefined. Filtering out those + # repositories at this step will reduce the number of "false negatives" the automated functional test framework produces. for tool_dict in tool_dicts: + failure_reason = '' + problem_found = False + tool_has_defined_tests = False + tool_has_test_files = False + missing_test_files = [] tool_count += 1 tool_id = tool_dict[ 'id' ] tool_version = tool_dict[ 'version' ] tool_guid = tool_dict[ 'guid' ] if verbosity >= 1: print "# Checking tool ID '%s' in changeset revision %s of %s." % ( tool_id, changeset_revision, name ) - # If there are no tests, this tool should not be tested, since the tool functional tests only report failure if the test itself fails, - # not if it's missing or undefined. Filtering out those repositories at this step will reduce the number of "false negatives" the - # automated functional test framework produces. - tool_has_tests = False defined_test_dicts = tool_dict.get( 'tests', None ) if defined_test_dicts is not None: # We need to inspect the <test> tags because the following tags... @@ -178,33 +189,26 @@ outputs = defined_test_dict.get( 'outputs', [] ) if inputs and outputs: # At least one tool within the repository has a valid <test> tag. - tool_has_tests = True + tool_has_defined_tests = True break - if tool_has_tests: - if verbosity >= 1: - print "# Tool ID '%s' in changeset revision %s of %s has one or more valid functional tests defined." % \ - ( tool_id, changeset_revision, name ) + if tool_has_defined_tests: + print "# Tool ID '%s' in changeset revision %s of %s has one or more valid functional tests defined." % \ + ( tool_id, changeset_revision, name ) has_tests += 1 else: - if verbosity >= 1: - print '# No functional tests defined for %s.' % tool_id + print '# No functional tests defined for %s.' % tool_id no_tests += 1 - failure_reason = '' - problem_found = False - missing_test_files = [] - has_test_files = False - if tool_has_tests and has_test_data: + if tool_has_defined_tests and revision_has_test_data: missing_test_files = check_for_missing_test_files( defined_test_dicts, test_data_path ) if missing_test_files: - if verbosity >= 1: - print "# Tool ID '%s' in changeset revision %s of %s is missing one or more required test files: %s" % \ - ( tool_id, changeset_revision, name, ', '.join( missing_test_files ) ) + print "# Tool id '%s' in changeset revision %s of %s is missing one or more required test files: %s" % \ + ( tool_id, changeset_revision, name, ', '.join( missing_test_files ) ) else: - has_test_files = True - if not has_test_data: + tool_has_test_files = True + if not revision_has_test_data: failure_reason += 'Repository does not have a test-data directory. ' problem_found = True - if not tool_has_tests: + if not tool_has_defined_tests: failure_reason += 'Functional test definitions missing for %s. ' % tool_id problem_found = True if missing_test_files: @@ -215,7 +219,8 @@ if problem_found: if test_errors not in missing_test_components: missing_test_components.append( test_errors ) - if tool_has_tests and has_test_files: + if tool_has_defined_tests and tool_has_test_files: + print '# Revision %s of %s owned by %s is a testable revision.' % ( changeset_revision, name, owner ) testable_revision = True # Remove the cloned repository path. This has to be done after the check for required test files, for obvious reasons. if os.path.exists( work_dir ): @@ -227,9 +232,9 @@ invalid_revisions += 1 print '# Some tools have problematic functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) if verbosity >= 1: - for invalid_test in missing_test_components: - if 'missing_components' in invalid_test: - print '# %s' % invalid_test[ 'missing_components' ] + for missing_test_component in missing_test_components: + if 'missing_components' in missing_test_component: + print '# %s' % missing_test_component[ 'missing_components' ] if not info_only: # Get or create the list of tool_test_results dictionaries. if repository_metadata.tool_test_results is not None: @@ -243,8 +248,9 @@ # install_and_test_tool_sed_repositories.sh script which will further populate the tool_test_results_dict. tool_test_results_dict = tool_test_results_dicts[ 0 ] if len( tool_test_results_dict ) <= 1: - # We can re-use the mostly empty tool_test_results_dict for this run, but we need to eliminate it from - # the list of tool_test_results_dicts since it will be re-inserted later. + # We can re-use the mostly empty tool_test_results_dict for this run because it is either empty or it contains only + # a test_environment entry. If we use it we need to temporarily eliminate it from the list of tool_test_results_dicts + # since it will be re-inserted later. tool_test_results_dict = tool_test_results_dicts.pop( 0 ) else: # The latest tool_test_results_dict has been populated with the results of a test run, so it cannot be used. @@ -284,6 +290,8 @@ # Even though some tools may be missing test components, it may be possible to test other tools. Since the # install and test framework filters out repositories marked as missing test components, we'll set it only if # no tools can be tested. + print '# Setting missing_test_components to True for revision %s of %s owned by %s because all tools are missing test components.' % \ + ( changeset_revision, name, owner ) repository_metadata.missing_test_components = True tool_test_results_dict[ 'missing_test_components' ] = missing_test_components # Store only the configured number of test runs. diff -r 864f8f4c466e4c031739549ea6a038dd70a4ed9a -r 024e7ca6c1a6023d49f4f63014185d14760faecf test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -363,6 +363,8 @@ """ error_message = '' latest_revision_only = '-check_all_revisions' not in sys.argv + if latest_revision_only: + log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' ) repository_dicts = [] params = urllib.urlencode( dict( do_not_test='false', downloadable='true', @@ -374,7 +376,6 @@ baseline_repository_dicts, error_message = json_from_url( api_url ) if error_message: return None, error_message - log.debug( 'The Tool Shed API returned %d metadata revisions for installation and testing.' % len( baseline_repository_dicts ) ) for baseline_repository_dict in baseline_repository_dicts: # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the # module that will generate the install methods. @@ -393,10 +394,6 @@ repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) else: repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - if latest_revision_only: - skipped_previous = ' and metadata revisions that are not the most recent' - else: - skipped_previous = '' if testing_single_repository: tsr_name = testing_single_repository[ 'name' ] tsr_owner = testing_single_repository[ 'owner' ] @@ -414,14 +411,15 @@ return repository_dicts, error_message return repository_dicts, error_message # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable. - log.debug( "Retrieved %d repositories from the API url: %s." % ( len( repository_dicts ), str( galaxy_tool_shed_url ) ) ) - if '-list_repositories' in sys.argv: - log.debug( "Repositories for testing:" ) - for repository_dict in repository_dicts: - log.debug( "Revision %s of repository %s owned by %s" % \ - ( str( repository_dict.get( 'changeset_revision', None ) ), \ - str( repository_dict.get( 'name', None ) ), \ - str( repository_dict.get( 'owner', None ) ) ) ) + log.debug( "The Tool Shed's API url...\n%s" % str( api_url ) ) + log.debug( "...retrieved %d repository revisions for testing." % len( repository_dicts ) ) + #if '-list_repositories' in sys.argv: + log.debug( "Repository revisions for testing:" ) + for repository_dict in repository_dicts: + log.debug( "Revision %s of repository %s owned by %s" % \ + ( str( repository_dict.get( 'changeset_revision', None ) ), \ + str( repository_dict.get( 'name', None ) ), \ + str( repository_dict.get( 'owner', None ) ) ) ) return repository_dicts, error_message def get_static_settings(): @@ -503,7 +501,7 @@ params = dict( tools_functionally_correct=False, do_not_test=False, test_install_error=True ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) # Since this repository is missing components, we do not want to test it, so deactivate it or uninstall it. # The deactivate flag is set to True if the environment variable GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES @@ -618,6 +616,7 @@ name = str( repository_dict[ 'name' ] ) owner = str( repository_dict[ 'owner' ] ) changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + log.debug( "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) ) # Populate the tool_test_results_dict. tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, encoded_repository_metadata_id ) if error_message: @@ -633,124 +632,122 @@ log.exception( "Invalid list of tool_test_results_dicts %s: %s" % ( str( tool_test_results_dicts ), str( e ) ) ) continue # See if this repository should be skipped for any reason. - skip_this_repository = False + this_repository_is_in_the_exclude_lost = False skip_reason = None for exclude_dict in exclude_list: reason = exclude_dict[ 'reason' ] exclude_repositories = exclude_dict[ 'repositories' ] if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: - skip_this_repository = True + this_repository_is_in_the_exclude_lost = True skip_reason = reason break - if skip_this_repository: + if this_repository_is_in_the_exclude_lost: tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) params = dict( tools_functionally_correct=False, do_not_test=False ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) - log.debug( "Not testing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) + log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \ + ( changeset_revision, name, owner ) ) else: + test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) + test_environment_dict = get_test_environment( test_environment_dict ) + # Add the current time as the approximate time that this test run occurs. A similar value will also be + # set to the repository_metadata.time_last_tested column, but we also store it here because the Tool Shed + # may be configured to store multiple test run results, so each must be associated with a time stamp. + now = time.strftime( "%Y-%m-%d %H:%M:%S" ) + test_environment_dict[ 'time_tested' ] = now + test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app ) + test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() ) + tool_test_results_dict[ 'test_environment' ] = test_environment_dict + tool_test_results_dict[ 'passed_tests' ] = [] + tool_test_results_dict[ 'failed_tests' ] = [] + tool_test_results_dict[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) + repository, error_message = install_repository( app, repository_dict ) if error_message: - log.debug( error_message ) + tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message + # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. + log.debug( 'Attempting to uninstall repository %s owned by %s.' % ( name, owner ) ) + try: + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + except Exception, e: + error_message = 'Unable to find installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) + log.exception( error_message ) + test_result = dict( tool_shed=galaxy_tool_shed_url, + name=name, + owner=owner, + changeset_revision=changeset_revision, + error_message=error_message ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) + params = dict( tools_functionally_correct=False, + test_install_error=True, + do_not_test=False ) + # TODO: do something useful with response_dict + response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) + try: + if deactivate: + # We are deactivating this repository and all of its repository dependencies. + deactivate_repository( app, repository_dict ) + else: + # We are uninstalling this repository and all of its repository dependencies. + uninstall_repository( app, repository_dict ) + except: + log.exception( 'Encountered error attempting to deactivate or uninstall %s.', str( repository_dict[ 'name' ] ) ) + results_dict[ 'repositories_failed_install' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) + log.debug( 'Repository %s failed to install correctly.' % str( name ) ) else: - test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) - test_environment_dict = get_test_environment( test_environment_dict ) - # Add the current time as the approximate time that this test run occurs. A similar value will also be - # set to the repository_metadata.time_last_tested column, but we also store it here because the Tool Shed - # may be configured to store multiple test run results, so each must be associated with a time stamp. - now = time.strftime( "%Y-%m-%d %H:%M:%S" ) - test_environment_dict[ 'time_tested' ] = now - test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app ) - test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() ) - tool_test_results_dict[ 'test_environment' ] = test_environment_dict - tool_test_results_dict[ 'passed_tests' ] = [] - tool_test_results_dict[ 'failed_tests' ] = [] - tool_test_results_dict[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) - repository, error_message = install_repository( app, repository_dict ) - if error_message: - tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message - # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. - log.debug( 'Attempting to uninstall repository %s owned by %s.' % ( name, owner ) ) + # Configure and run functional tests for this repository. This is equivalent to sh run_functional_tests.sh -installed + remove_install_tests() + log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) + # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository + # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, + # and the tools_functionally_correct flag to False, as well as updating tool_test_results. + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + has_test_data, shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, + from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + # Add an empty 'missing_test_results' entry if it is missing from the tool_test_results_dict. The + # ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered information in the + # 'missing_test_components' entry of the tool_test_results_dict dictionary for repositories that are + # missing test components. + if 'missing_test_components' not in tool_test_results_dict: + tool_test_results_dict[ 'missing_test_components' ] = [] + missing_tool_dependencies = get_missing_tool_dependencies( repository ) + if missing_tool_dependencies or repository.missing_repository_dependencies: + results_dict = handle_missing_dependencies( app, + repository, + missing_tool_dependencies, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + results_dict ) + else: + # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional + # test framework can find it. + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) + log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), str( shed_tools_dict ) ) ) try: - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + results_dict = test_repository_tools( app, + repository, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + results_dict ) except Exception, e: - error_message = 'Unable to find installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) - log.exception( error_message ) - test_result = dict( tool_shed=galaxy_tool_shed_url, - name=name, - owner=owner, - changeset_revision=changeset_revision, - error_message=error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - params = dict( tools_functionally_correct=False, - test_install_error=True, - do_not_test=False ) - # TODO: do something usefule with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) - try: - if deactivate: - # We are deactivating this repository and all of its repository dependencies. - deactivate_repository( app, repository_dict ) - else: - # We are uninstalling this repository and all of its repository dependencies. - uninstall_repository( app, repository_dict ) - except: - log.exception( 'Encountered error attempting to deactivate or uninstall %s.', str( repository_dict[ 'name' ] ) ) - results_dict[ 'repositories_failed_install' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - log.debug( 'Repository %s failed to install correctly.' % str( name ) ) - else: - # Configure and run functional tests for this repository. This is equivalent to sh run_functional_tests.sh -installed - remove_install_tests() - log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) - # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository - # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, - # and the tools_functionally_correct flag to False, as well as updating tool_test_results. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) - has_test_data, shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, - from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) - # Add an empty 'missing_test_results' entry if it is missing from the tool_test_results_dict. The - # ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered information in the - # 'missing_test_components' entry of the tool_test_results_dict dictionary for repositories that are - # missing test components. - if 'missing_test_components' not in tool_test_results_dict: - tool_test_results_dict[ 'missing_test_components' ] = [] - missing_tool_dependencies = get_missing_tool_dependencies( repository ) - if missing_tool_dependencies or repository.missing_repository_dependencies: - results_dict = handle_missing_dependencies( app, - repository, - missing_tool_dependencies, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - results_dict ) - else: - # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional - # test framework can find it. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) - log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), str( shed_tools_dict ) ) ) - try: - results_dict = test_repository_tools( app, - repository, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - results_dict ) - except Exception, e: - exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) - log.exception( exception_message ) - tool_test_results_dict[ 'failed_tests' ].append( exception_message ) - # Record the status of this repository in the tool shed. - params = dict( tools_functionally_correct=False, - do_not_test=False, - test_install_error=False ) - # TODO: do something usefule with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) - results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - total_repositories_tested += 1 + exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) + log.exception( exception_message ) + tool_test_results_dict[ 'failed_tests' ].append( exception_message ) + # Record the status of this repository in the tool shed. + params = dict( tools_functionally_correct=False, + do_not_test=False, + test_install_error=False ) + # TODO: do something useful with response_dict + response_dict = register_test_result( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params ) + results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) + total_repositories_tested += 1 results_dict[ 'total_repositories_tested' ] = total_repositories_tested return results_dict, error_message @@ -1073,13 +1070,14 @@ exclude_count += 1 exclude_dict[ 'repositories' ].append( repository_tuple ) exclude_list.append( exclude_dict ) - log.debug( '%s repositories will be excluded from testing...' % str( exclude_count ) ) - if '-list_repositories' in sys.argv: - for name, owner, changeset_revision in exclude_verbose: - if changeset_revision: - log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) ) - else: - log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) + log.debug( 'The xml document %s containing the exclude list %s defines the following %s repositories to be excluded from testing...' % \ + ( str( xml_filename ), str( exclude_count ) ) ) + #if '-list_repositories' in sys.argv: + for name, owner, changeset_revision in exclude_verbose: + if changeset_revision: + log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) ) + else: + log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) return exclude_list def register_test_result( url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ): @@ -1209,7 +1207,7 @@ params = dict( tools_functionally_correct=True, do_not_test=False, test_install_error=False ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( str( changeset_revision ), str( name ) ) ) else: @@ -1220,7 +1218,7 @@ params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) - # TODO: do something usefule with response_dict + # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed successfully but did not pass functional tests.' % \ ( str( changeset_revision ), str( name ) ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 29 Nov '13

29 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5b8c91e41836/ Changeset: 5b8c91e41836 User: jmchilton Date: 2013-11-29 04:23:42 Summary: Rework handling of complex package dependencies. Now symbolically linking to previously generated env.sh files instead of recreating them from scratch using install_and_build_package_via_fabric after inferring previous install parameters by parsing out existing env.sh file. This has several advantages: - Fixes problems where setup_* actions were not being used as complex dependency package properly (previous code assumed only set_environment and setup_virtualenv actions would work in this case). Problem reported by Bjoern Gruening. - Handles deployer modified env.sh files and allows deployers to modify fewer env.sh. - The way install_util was pulling values out of existing env.sh and recreating the files was creating a dependency on each future version of the install code with the specific implementations of past install procedures - new environment variables could not be added to setup_ruby_environment for instance if it was realized that they were needed. Turns out the biggest difference between this and the previous implementation is related to handling of complex package dependencies where the dependent repository is not installed. Previously, the Galaxy install code would have attempted to create an env.sh file with the path modifications as they would look if it had been installed - i.e. with completely invalid paths. My translation of this behavior is to write an invalid symbolic link to the env.sh file that would be installed. I am not sure this has any practical consequences. I would like to understand better why handling complex tool dependencies on dependent repositories that are not installed is done at all. Most package management systems, will prevent you from installing a package if dependent packages are not installed. This isn't to say what Galaxy is doing is wrong, it is just atypical and I would like to understand the use cases that lead to the decision better. Affected #: 2 files diff -r 9ff030d0daee11b2187d9784a8b0a57742a671c2 -r 5b8c91e4183664c90f4d95699ab971e674ffd67d lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3471,6 +3471,29 @@ def can_reinstall_or_activate( self ): return self.deleted + @property + def installing( self ): + """ + Used to determine if tool dependencies can denote this repository as + installing. + """ + return self.status not in [ self.installation_status.DEACTIVATED, + self.installation_status.UNINSTALLED, + self.installation_status.ERROR, + self.installation_status.INSTALLED, + self.installation_status.NEW, + ] + + @property + def installation_complete( self ): + """ + Used to determine if tool dependency installations can proceed. + Installed artifacts must be available on disk. + """ + return self.status in [ self.installation_status.DEACTIVATED, + self.installation_status.INSTALLED, + ] + def to_dict( self, view='collection', value_mapper=None ): if value_mapper is None: value_mapper = {} diff -r 9ff030d0daee11b2187d9784a8b0a57742a671c2 -r 5b8c91e4183664c90f4d95699ab971e674ffd67d lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -40,6 +40,70 @@ raise Exception( message ) return None + +def find_complex_dependency_package( app, dependent_install_dir, required_install_dir, tool_shed_repository, required_repository, package_name, package_version, tool_dependencies_config ): + """ + """ + tool_dependencies = [] + if not os.path.exists( dependent_install_dir ): + os.makedirs( dependent_install_dir ) + env_file = None + if tool_dependencies_config: + required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config ) + if required_td_tree: + required_td_root = required_td_tree.getroot() + for required_td_elem in required_td_root: + # Find the appropriate package name and version. + if required_td_elem.tag == 'package': + # <package name="bwa" version="0.5.9"> + required_td_package_name = required_td_elem.get( 'name', None ) + required_td_package_version = required_td_elem.get( 'version', None ) + if required_td_package_name == package_name and required_td_package_version == package_version: + tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=package_name, + version=package_version, + type='package', + status=app.model.ToolDependency.installation_status.NEVER_INSTALLED, + set_status=True ) + + if required_repository.installing: + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLING ) + # What happens if dependent repository fails or is + # uninstalled during this process. + env_file = required_repository_package_env( app, package_name, package_version, required_repository ) + if required_repository.installation_complete: + if not os.path.exists( env_file ): + error_message = 'env.sh file %s for package %s in dependendent repository could not be found. Required repository has status %s.' % ( package_name, env_file, required_repository.status ) + tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, + tool_dependency, + error_message, + remove_installation_path=False ) + else: + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLED ) + else: + # Ekk - handling tool depednencies for a dependent + # repository that is not installed. + # + # Go ahead a return the env.sh file - Galaxy will + # proceed to create an invalid symbolic link. + # This is subtle-ly different than the previous + # behavior which would have recreated an env.sh + # from the the required repository's + # tool_dependencies.xml but since it was not + # installed all of the values inside would be + # invalid path modifications. Either way, this file + # is junk until the required repository is + # installed properly. + pass + tool_dependencies.append( tool_dependency ) + return tool_dependencies, env_file + + def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ): """Return the absolute path to a specified disk file contained in a repository.""" stripped_file_name = strip_path( file_name ) @@ -91,6 +155,7 @@ text = common_util.tool_shed_get( app, tool_shed_url, url ) return text + def handle_complex_repository_dependency_for_package( app, elem, package_name, package_version, tool_shed_repository ): handled_tool_dependencies = [] tool_shed = elem.attrib[ 'toolshed' ] @@ -125,8 +190,7 @@ tool_dependency_version=package_version ) # Set this dependent repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package. # We can get everything we need from the discovered installed required_repository. - if required_repository.status in [ app.model.ToolShedRepository.installation_status.DEACTIVATED, - app.model.ToolShedRepository.installation_status.INSTALLED ]: + if required_repository.installation_complete: if not os.path.exists( required_repository_package_install_dir ): print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) repo_files_dir = required_repository.repo_files_directory( app ) @@ -156,22 +220,26 @@ required_repository_owner, required_repository_changeset_revision ) config_to_use = tmp_filename - tool_dependencies, actions_dict = populate_actions_dict( app=app, - dependent_install_dir=dependent_install_dir, - required_install_dir=required_repository_package_install_dir, - tool_shed_repository=tool_shed_repository, - required_repository=required_repository, - package_name=package_name, - package_version=package_version, - tool_dependencies_config=config_to_use ) + + tool_dependencies, package_env_sh_file = find_complex_dependency_package( + app=app, + dependent_install_dir=dependent_install_dir, + required_install_dir=required_repository_package_install_dir, + tool_shed_repository=tool_shed_repository, + required_repository=required_repository, + package_name=package_name, + package_version=package_version, + tool_dependencies_config=config_to_use + ) + if package_env_sh_file: + os.symlink( package_env_sh_file, os.path.join( dependent_install_dir, "env.sh" ) ) if tmp_filename: try: os.remove( tmp_filename ) except: pass for tool_dependency in tool_dependencies: - # Install and build the package via fabric and update the tool_dependency record accordingly.. - tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) + tool_dependency = __mark_tool_dependency_installed( app, tool_dependency) handled_tool_dependencies.append( tool_dependency ) else: message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ @@ -179,113 +247,6 @@ raise Exception( message ) return handled_tool_dependencies -def handle_set_environment_entry_for_package( app, install_dir, tool_shed_repository, package_name, package_version, elem, required_repository ): - """ - Populate a list of actions for creating an env.sh file for a dependent repository. The received elem is the <package> tag set associated - with the tool-dependencies.xml file for one of the received tool_shed_repository's repository dependency. - """ - action_dict = {} - actions = [] - tool_dependencies = [] - for package_elem in elem: - if package_elem.tag == 'install': - # Create the new tool_dependency record in the database. - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=package_name, - version=package_version, - type='package', - status=app.model.ToolDependency.installation_status.NEVER_INSTALLED, - set_status=True ) - # Get the installation method version from a tag like: <install version="1.0"> - package_install_version = package_elem.get( 'version', '1.0' ) - if package_install_version == '1.0': - # Update the tool dependency's status. - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLING ) - # Since the required tool dependency is installed for a repository dependency, we first need to inspect the <actions> tag set to find - # the <action type="set_environment"> tag. - env_var_dicts = [] - for actions_elem in package_elem: - for action_elem in actions_elem: - action_type = action_elem.get( 'type', 'shell_command' ) - if action_type == 'set_environment': - # <action type="set_environment"> - # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> - # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - # </action> - for env_elem in action_elem: - if env_elem.tag == 'environment_variable': - env_var_dict = td_common_util.create_env_var_dict( env_elem, tool_dependency_install_dir=install_dir ) - if env_var_dict: - if env_var_dict not in env_var_dicts: - env_var_dicts.append( env_var_dict ) - elif action_type == 'setup_virtualenv': - # Add the virtualenv's site-packages to PYTHONPATH and bin to PATH. This is a bit hackish. - site_packages_command = "%s -c 'import os, sys; print os.path.join(sys.prefix, \"lib\", \"python\" + sys.version[:3], \"site-packages\")'" % os.path.join( install_dir, "venv", "bin", "python" ) - output = fabric_util.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) - if output.return_code: - log.error( 'Tool dependency %s includes a setup_virtualenv action but venv python is broken: ' % \ - ( str( tool_dependency.name ), str( output.stderr ) ) ) - elif not os.path.exists( output.stdout ): - log.error( "virtualenv's site-packages directory '%s' does not exist", str( output.stdout ) ) - else: - env_var_dicts.append( dict( name="PYTHONPATH", action="prepend_to", value=output.stdout ) ) - env_var_dicts.append( dict( name="PATH", action="prepend_to", value=os.path.join( install_dir, 'venv', 'bin' ) ) ) - if env_var_dicts: - if required_repository.status in [ app.model.ToolShedRepository.installation_status.INSTALLED, - app.model.ToolShedRepository.installation_status.DEACTIVATED ]: - # Handle the case where we have an installed required repository due to the prior_installation_required = True - # setting in the received tool_shed_repository's tool_dependencies.xml file and the required repository's - # tool_dependencies.xml file may include the use of the $ENV[] variable inheritance feature. To handle this, - # we will replace the current "value" entries in each env_var_dict with the actual path taken from the env.sh - # file generated for the installed required repository. Each env_var_dict currently looks something like this: - # {'action': 'append_to', 'name': 'LD_LIBRARY_PATH', 'value': '$BOOST_ROOT_DIR/lib/'} - # We'll read the contents of the received required_repository's env.sh file and replace the 'value' entry of - # each env_var_dict with the associated value in the env.sh file. - new_env_var_dicts = [] - env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, - repository_name=required_repository.name, - repository_owner=required_repository.owner, - repository_changeset_revision=required_repository.installed_changeset_revision, - tool_dependency_type='package', - tool_dependency_name=package_name, - tool_dependency_version=package_version ) - env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) - if os.path.exists( env_sh_file_path ): - for i, line in enumerate( open( env_sh_file_path, 'r' ) ): - env_var_dict = env_var_dicts[ i ] - action = env_var_dict.get( 'action', None ) - name = env_var_dict.get( 'name', None ) - value = env_var_dict.get( 'value', None ) - if action and name and value: - new_value = parse_env_shell_entry( action, name, value, line ) - env_var_dict[ 'value' ] = new_value - new_env_var_dicts.append( env_var_dict ) - else: - error_message = 'Invalid file %s specified, ignoring set_environment_for_install action.' % str( env_sh_file_path ) - tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, - tool_dependency, - error_message, - remove_installation_path=False ) - action_dict[ 'environment_variable' ] = new_env_var_dicts - else: - action_dict[ 'environment_variable' ] = env_var_dicts - actions.append( ( 'set_environment', action_dict ) ) - if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, - app.model.ToolDependency.installation_status.INSTALLED ]: - # Update the tool dependency's status. - tool_dependency = \ - tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLED ) - # Accumulate processed tool dependencies to return to the caller. - tool_dependencies.append( tool_dependency ) - else: - raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' ) - return tool_dependencies, actions - return tool_dependencies, actions def install_and_build_package_via_fabric( app, tool_dependency, actions_dict ): sa_session = app.model.context.current @@ -301,17 +262,10 @@ tool_dependency, error_message, remove_installation_path=False ) - if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, - app.model.ToolDependency.installation_status.INSTALLED ]: - log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ - ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) ) - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.model.ToolDependency.installation_status.INSTALLED, - error_message=None, - remove_from_disk=False ) + tool_dependency = __mark_tool_dependency_installed( app, tool_dependency) return tool_dependency + def install_package( app, elem, tool_shed_repository, tool_dependencies=None ): # The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository. sa_session = app.model.context.current @@ -821,60 +775,22 @@ tool_dependency = install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) return tool_dependency -def parse_env_shell_entry( action, name, value, line ): - new_value = value - var_name = '$%s' % name - tmp_value = line.split( '=' )[ 1 ] - if action == 'prepend_to': - # PATH=/test/package_rdkit_2012_12/62ebd7bb637a/rdkit/bin:$PATH; export PATH - new_value = tmp_value.split( ':%s' % var_name )[ 0 ] - elif action == 'set_to': - # RDBASE=test/package_rdkit_2012_12/62ebd7bb637a/rdkit; export RDBASE - new_value = tmp_value.split( ';' )[ 0 ] - elif action == 'append_to': - # LD_LIBRARY_PATH=$LD_LIBRARY_PATH:test/package_rdkit_2012_12/62ebd7bb637a/rdkit/lib/; export LD_LIBRARY_PATH - new_value = tmp_value.split( ':' )[ 1 ] - new_value = new_value.split( ';' )[ 0 ] - return new_value -def populate_actions_dict( app, dependent_install_dir, required_install_dir, tool_shed_repository, required_repository, package_name, package_version, tool_dependencies_config ): +# TODO: Move to tool_dependency_util? +def required_repository_package_env( app, package_name, package_version, required_repository ): """ - Populate an actions dictionary that can be sent to fabric_util.install_and_build_package. This method handles the scenario where a tool_dependencies.xml - file defines a complex repository dependency. In this case, the tool dependency package will be installed in a separate repository and the tool dependency - defined for the dependent repository will use an environment_variable setting defined in it's env.sh file to locate the required package. This method - basically does what the install_via_fabric method does, but restricts it's activity to the <action type="set_environment"> tag set within the required - repository's tool_dependencies.xml file. + Return path to env.sh file in required repository if the required repository has been installed. """ - sa_session = app.model.context.current - if not os.path.exists( dependent_install_dir ): - os.makedirs( dependent_install_dir ) - actions_dict = dict( install_dir=dependent_install_dir ) - if package_name: - actions_dict[ 'package_name' ] = package_name - tool_dependencies = [] - action_dict = {} - if tool_dependencies_config: - required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - if required_td_tree: - required_td_root = required_td_tree.getroot() - for required_td_elem in required_td_root: - # Find the appropriate package name and version. - if required_td_elem.tag == 'package': - # <package name="bwa" version="0.5.9"> - required_td_package_name = required_td_elem.get( 'name', None ) - required_td_package_version = required_td_elem.get( 'version', None ) - if required_td_package_name==package_name and required_td_package_version==package_version: - tool_dependencies, actions = handle_set_environment_entry_for_package( app=app, - install_dir=required_install_dir, - tool_shed_repository=tool_shed_repository, - package_name=package_name, - package_version=package_version, - elem=required_td_elem, - required_repository=required_repository ) - if actions: - actions_dict[ 'actions' ] = actions - break - return tool_dependencies, actions_dict + env_sh_file_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, + repository_name=required_repository.name, + repository_owner=required_repository.owner, + repository_changeset_revision=required_repository.installed_changeset_revision, + tool_dependency_type='package', + tool_dependency_name=package_name, + tool_dependency_version=package_version ) + env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) + return env_sh_file_path + def run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=None, **kwd ): """ @@ -1019,3 +935,17 @@ for arg in args: parts.append( arg.strip( '/' ) ) return '/'.join( parts ) + + +# TODO: Move to tool_dependency_util? +def __mark_tool_dependency_installed( app, tool_dependency ): + if tool_dependency.status not in [ app.model.ToolDependency.installation_status.ERROR, + app.model.ToolDependency.installation_status.INSTALLED ]: + log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ + ( str( tool_dependency.name ), str( tool_dependency.status ), str( app.model.ToolDependency.installation_status.INSTALLED ) ) ) + tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=app.model.ToolDependency.installation_status.INSTALLED, + error_message=None, + remove_from_disk=False ) + return tool_dependency https://bitbucket.org/galaxy/galaxy-central/commits/864f8f4c466e/ Changeset: 864f8f4c466e User: jmchilton Date: 2013-11-29 04:23:42 Summary: Eliminate pre-bashisms from tool shed install action handlers. Affected #: 1 file diff -r 5b8c91e4183664c90f4d95699ab971e674ffd67d -r 864f8f4c466e4c031739549ea6a038dd70a4ed9a lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -390,7 +390,7 @@ with lcd( current_dir ): with settings( warn_only=True ): for tarball_name in tarball_names: - cmd = '''export PATH=$PATH:$R_HOME/bin && export R_LIBS=$INSTALL_DIR && + cmd = '''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS; && Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % ( str( tarball_name ) ) cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) @@ -432,24 +432,24 @@ gem, gem_version = ruby_package_tup if os.path.isfile( gem ): # we assume a local shipped gem file - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install --local %s''' % ( gem ) elif gem.find( '://' ) != -1: # We assume a URL to a gem file. url = gem gem_name = url.split( '/' )[ -1 ] td_common_util.url_download( work_dir, gem_name, url, extract=False ) - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install --local %s ''' % ( gem_name ) else: # gem file from rubygems.org with or without version number if gem_version: # version number was specified - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install %s --version "=%s"''' % ( gem, gem_version) else: # no version number given - cmd = '''export PATH=$PATH:$RUBY_HOME/bin && export GEM_HOME=$INSTALL_DIR && + cmd = '''PATH=$PATH:$RUBY_HOME/bin; export PATH; GEM_HOME=$INSTALL_DIR; export GEM_HOME; gem install %s''' % ( gem ) cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) @@ -490,7 +490,7 @@ for perl_package in perl_packages: # If set to a true value then MakeMaker's prompt function will always # return the default without waiting for user input. - cmd = '''export PERL_MM_USE_DEFAULT=1 && ''' + cmd = '''PERL_MM_USE_DEFAULT=1; export PERL_MM_USE_DEFAULT; ''' if perl_package.find( '://' ) != -1: # We assume a URL to a gem file. url = perl_package Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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