June 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: natefoo: Fix Ctrl+C (make the UpdateRepositoryManager's updater thread a daemon).
by commits-noreply＠bitbucket.org 25 Jun '14

25 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1802e93a4f18/ Changeset: 1802e93a4f18 User: natefoo Date: 2014-06-26 02:07:58 Summary: Fix Ctrl+C (make the UpdateRepositoryManager's updater thread a daemon). Affected #: 1 file diff -r 6b672fb120994f308ce7914993418e67770aae14 -r 1802e93a4f1823f307de534d9b6ce73d911f6538 lib/tool_shed/galaxy_install/update_repository_manager.py --- a/lib/tool_shed/galaxy_install/update_repository_manager.py +++ b/lib/tool_shed/galaxy_install/update_repository_manager.py @@ -19,6 +19,7 @@ self.running = True self.sleeper = Sleeper() self.restarter = threading.Thread( target=self.__restarter ) + self.restarter.daemon = True self.restarter.start() self.seconds_to_sleep = int( app.config.hours_between_check * 3600 ) 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: davebgx: Enhance the tool shed repository API controller to allow filtering by owner's username or repository name.
by commits-noreply＠bitbucket.org 25 Jun '14

25 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6b672fb12099/ Changeset: 6b672fb12099 User: davebgx Date: 2014-06-25 21:07:43 Summary: Enhance the tool shed repository API controller to allow filtering by owner's username or repository name. Affected #: 1 file diff -r 8a161a3990b5e19dd2b324323ba934f8a5f37c8b -r 6b672fb120994f308ce7914993418e67770aae14 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -7,6 +7,7 @@ from galaxy import eggs from galaxy import util from galaxy import web +from galaxy.model.orm import and_ from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import HTTPBadRequest from galaxy.web.framework.helpers import time_ago @@ -297,16 +298,28 @@ return return_dict @web.expose_api_anonymous - def index( self, trans, deleted=False, **kwd ): + def index( self, trans, deleted=False, owner=None, name=None, **kwd ): """ GET /api/repositories + + :param deleted: True/False, displays repositories that are or are not set to deleted. + :param owner: the owner's public username. + :param name: the repository name. + Displays a collection (list) of repositories. """ # Example URL: http://localhost:9009/api/repositories repository_dicts = [] deleted = util.asbool( deleted ) + clause_list = [ and_( trans.app.model.Repository.table.c.deprecated == False, + trans.app.model.Repository.table.c.deleted == deleted ) ] + if owner is not None: + clause_list.append( and_( trans.app.model.User.table.c.username == owner, + trans.app.model.Repository.table.c.user_id == trans.app.model.User.table.c.id ) ) + if name is not None: + clause_list.append( trans.app.model.Repository.table.c.name == name ) for repository in trans.sa_session.query( trans.app.model.Repository ) \ - .filter( trans.app.model.Repository.table.c.deleted == deleted ) \ + .filter( *clause_list ) \ .order_by( trans.app.model.Repository.table.c.name ): repository_dict = repository.to_dict( view='collection', value_mapper=self.__get_value_mapper( trans ) ) 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: Another docfix for recent local job runner changes.
by commits-noreply＠bitbucket.org 25 Jun '14

25 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8a161a3990b5/ Changeset: 8a161a3990b5 User: jmchilton Date: 2014-06-25 16:11:26 Summary: Another docfix for recent local job runner changes. Affected #: 1 file diff -r 1c40abf8bc5b7555dd276e540f487f8c288da4b2 -r 8a161a3990b5e19dd2b324323ba934f8a5f37c8b universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -804,7 +804,7 @@ # the cluster that should be sourced by the user to set up the environment # prior to running tools. This can be especially useful for running jobs as # the actual user, to remove the need to configure each user's environment -# individually. This only affects cluster jobs, not local jobs. +# individually. #environment_setup_file = 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: 2 new changesets
by commits-noreply＠bitbucket.org 25 Jun '14

25 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/75c63b579ccd/ Changeset: 75c63b579ccd User: jmchilton Date: 2014-06-25 15:01:52 Summary: Add documentation about local runner destination option embed_metadata_in_job. Affected #: 1 file diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r 75c63b579ccdd63e0558dd9aefce7786677dbacd job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -102,6 +102,12 @@  + <param id="embed_metadata_in_job">True</param> + <job_metrics /> + <param id="embed_metadata_in_job">True</param> + <job_metrics /><!-- Above element demonstrates embedded job metrics definition - see job_metrics_conf.xml.sample for full documentation on possible nested 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: carlfeberhard: Fix: phantomjs apparently lacks the bind fn on the Function prototype - correct failures in history-panel (line 252) by using underscore bind instead; up the standard upload timeout interval for api tests
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aff21e09778e/ Changeset: aff21e09778e User: carlfeberhard Date: 2014-06-24 23:02:23 Summary: Fix: phantomjs apparently lacks the bind fn on the Function prototype - correct failures in history-panel (line 252) by using underscore bind instead; up the standard upload timeout interval for api tests Affected #: 2 files diff -r ae31e175f1cd836e89324a57d2c4276c5091f95f -r aff21e09778ece1bdbe987a4dad2adb6a26e5447 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -249,7 +249,7 @@ actions.push( { // TODO: Only show quick pair if two things selected. html: _l( 'Build List of Dataset Pairs (Experimental)' ), - func: panel._showPairedCollectionModal.bind( panel ) + func: _.bind( panel._showPairedCollectionModal, panel ) }); return new PopupMenu( $where.find( '.history-dataset-action-popup-btn' ), actions ); }, diff -r ae31e175f1cd836e89324a57d2c4276c5091f95f -r aff21e09778ece1bdbe987a4dad2adb6a26e5447 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -555,7 +555,7 @@ }; /** amount of time allowed to upload a file (before erroring) */ -ToolsAPI.prototype.DEFAULT_UPLOAD_TIMEOUT = 12000; +ToolsAPI.prototype.DEFAULT_UPLOAD_TIMEOUT = 30 * 1000; /** add two casperjs steps - upload a file, wait for the job to complete, and run 'then' when they are */ ToolsAPI.prototype.thenUpload = function thenUpload( historyId, options, then ){ @@ -569,6 +569,9 @@ this.debug( 'uploadedId: ' + uploadedId ); }); + spaceghost.debug( '---------------------------------------------------------- timeout: ' + ( options.timeout || spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ) ); + spaceghost.debug( 'timeout: ' + options.timeout ); + spaceghost.debug( 'timeout: ' + spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ); spaceghost.then( function(){ this.waitFor( function testHdaState(){ 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: carlfeberhard: Style fix: use MS/IE specific syntax for flexbox to correct layout of paired-collection-creator in IE10 (Note: IE9 has no flexbox and this interface can't be used with it)
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ae31e175f1cd/ Changeset: ae31e175f1cd User: carlfeberhard Date: 2014-06-24 22:11:57 Summary: Style fix: use MS/IE specific syntax for flexbox to correct layout of paired-collection-creator in IE10 (Note: IE9 has no flexbox and this interface can't be used with it) Affected #: 2 files diff -r 17fbd073d94df628997df9df5af7d1de077bf82a -r ae31e175f1cd836e89324a57d2c4276c5091f95f static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1367,13 +1367,13 @@ .collection-creator .scroll-container{overflow:auto} .collection-creator .truncate{overflow:hidden;white-space:nowrap;text-overflow:ellipsis} .collection-creator .empty-message{color:grey;font-style:italic} -.collection-creator.flex-row-container,.collection-creator .flex-row-container,.collection-creator .flex-column-container{display:-webkit-box;display:-webkit-flex;display:flex;-webkit-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;align-content:stretch} -.collection-creator.flex-row-container,.collection-creator .flex-row-container{-webkit-flex-direction:column;flex-direction:column} -.collection-creator .flex-row{-webkit-flex:1 auto;flex:1 0 auto} -.collection-creator .flex-row.no-flex{-webkit-flex:0 auto;flex:0 0 auto} -.collection-creator .flex-column-container{-webkit-flex-direction:row;flex-direction:row} -.collection-creator .flex-column{-webkit-flex:1 auto;flex:1 1 auto} -.collection-creator .flex-column.no-flex{-webkit-flex:0 auto;flex:0 0 auto} +.collection-creator.flex-row-container,.collection-creator .flex-row-container,.collection-creator .flex-column-container{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;-webkit-align-items:stretch;-ms-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;-ms-align-content:stretch;align-content:stretch} +.collection-creator.flex-row-container,.collection-creator .flex-row-container{-webkit-flex-direction:column;-ms-flex-direction:column;flex-direction:column} +.collection-creator .flex-row{-webkit-flex:1 auto;-ms-flex:1 auto;flex:1 0 auto} +.collection-creator .flex-row.no-flex{-webkit-flex:0 auto;-ms-flex:0 auto;flex:0 0 auto} +.collection-creator .flex-column-container{-webkit-flex-direction:row;-ms-flex-direction:row;flex-direction:row} +.collection-creator .flex-column{-webkit-flex:1 auto;-ms-flex:1 auto;flex:1 1 auto} +.collection-creator .flex-column.no-flex{-webkit-flex:0 auto;-ms-flex:0 auto;flex:0 0 auto} .collection-creator .choose-filters .help{margin-bottom:2px;font-size:90%;color:grey} .collection-creator .choose-filters button{width:100%;margin-top:2px} .collection-creator .header .alert{display:none} diff -r 17fbd073d94df628997df9df5af7d1de077bf82a -r ae31e175f1cd836e89324a57d2c4276c5091f95f static/style/src/less/ui/paired-collection-creator.less --- a/static/style/src/less/ui/paired-collection-creator.less +++ b/static/style/src/less/ui/paired-collection-creator.less @@ -44,11 +44,15 @@ .flex-column-container { display: -webkit-box; display: -webkit-flex; + display: -ms-flexbox; display: flex; -webkit-align-items: stretch; + -ms-align-items: stretch; align-items: stretch; + -webkit-align-content: stretch; + -ms-align-content: stretch; align-content: stretch; } @@ -56,28 +60,34 @@ &.flex-row-container, .flex-row-container { -webkit-flex-direction: column; + -ms-flex-direction: column; flex-direction: column; } .flex-row { -webkit-flex: 1 auto; + -ms-flex: 1 auto; flex: 1 0 auto; } .flex-row.no-flex { -webkit-flex: 0 auto; + -ms-flex: 0 auto; flex: 0 0 auto; } // a series of horizontal elements that will expand to fill available space .flex-column-container { -webkit-flex-direction: row; + -ms-flex-direction: row; flex-direction: row; } .flex-column { -webkit-flex: 1 auto; + -ms-flex: 1 auto; flex: 1 1 auto; } .flex-column.no-flex { -webkit-flex: 0 auto; + -ms-flex: 0 auto; flex: 0 0 auto; } 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: carlfeberhard: Style fix: use Safari/webkit specific syntax for flexbox to correct layout of paired-collection-creator in Safari
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/17fbd073d94d/ Changeset: 17fbd073d94d User: carlfeberhard Date: 2014-06-24 21:46:12 Summary: Style fix: use Safari/webkit specific syntax for flexbox to correct layout of paired-collection-creator in Safari Affected #: 5 files diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/scripts/mvc/collection/dataset-collection-edit.js --- a/static/scripts/mvc/collection/dataset-collection-edit.js +++ b/static/scripts/mvc/collection/dataset-collection-edit.js @@ -17,7 +17,7 @@ // ......................................................................... edit attr, delete /** Render icon-button group for the common, most easily accessed actions. - * Overrides _render_titleButtons to include editting related buttons. + * Overrides _render_titleButtons to include editing related buttons. * @see DatasetCollectionBaseView#_render_titleButtons * @returns {jQuery} rendered DOM */ diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -7,6 +7,8 @@ */ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ + className: 'collection-creator flex-row-container', + /** set up initial options, instance vars, behaviors, and autopair (if set to do so) */ initialize : function( attributes ){ //console.debug( '-- PairedCollectionCreator:', attributes ); @@ -541,7 +543,8 @@ /** render the entire interface */ render : function( speed, callback ){ //console.debug( '-- _render' ); - this.$el.empty().addClass( 'collection-creator' ).html( PairedCollectionCreator.templates.main() ); + //this.$el.empty().html( PairedCollectionCreator.templates.main() ); + this.$el.empty().html( PairedCollectionCreator.templates.main() ); this._renderHeader( speed ); this._renderMiddle( speed ); this._renderFooter( speed ); @@ -1191,9 +1194,9 @@ PairedCollectionCreator.templates = PairedCollectionCreator.templates || { /** the skeleton */ main : _.template([ - '<div class="header"></div>', - '<div class="middle"></div>', - '<div class="footer">' + '<div class="header flex-row no-flex"></div>', + '<div class="middle flex-row flex-row-container"></div>', + '<div class="footer flex-row no-flex">' ].join('')), /** the header (not including help text) */ @@ -1209,7 +1212,7 @@ '<span class="alert-message"></span>', '</div>', - '<div class="column-headers vertically-spaced row-flex-container">', + '<div class="column-headers vertically-spaced flex-column-container">', '<div class="forward-column flex-column column">', '<div class="column-header">', '<div class="column-title">', @@ -1221,7 +1224,7 @@ '</div>', '</div>', '</div>', - '<div class="paired-column flex-column column">', + '<div class="paired-column flex-column no-flex column">', '<div class="column-header">', '<a class="choose-filters-link" href="javascript:void(0)">', _l( 'Choose filters' ), @@ -1250,11 +1253,12 @@ /** the middle: unpaired, divider, and paired */ middle : _.template([ - '<div class="unpaired-columns row-flex-container scroll-container">', + // contains two flex rows (rows that fill available space) and a divider btwn + '<div class="unpaired-columns flex-column-container scroll-container flex-row">', '<div class="forward-column flex-column column">', '<ol class="column-datasets"></ol>', '</div>', - '<div class="paired-column flex-column column">', + '<div class="paired-column flex-column no-flex column">', '<ol class="column-datasets"></ol>', '</div>', '<div class="reverse-column flex-column column">', @@ -1272,11 +1276,11 @@ '</a>', '</div>', '</div>', - '<div class="paired-columns row-flex-container scroll-container">', + '<div class="paired-columns flex-column-container scroll-container flex-row">', '<div class="forward-column flex-column column">', '<ol class="column-datasets"></ol>', '</div>', - '<div class="paired-column flex-column column">', + '<div class="paired-column flex-column no-flex column">', '<ol class="column-datasets"></ol>', '</div>', '<div class="reverse-column flex-column column">', diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.View.extend(a.LoggableMixin).extend({initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return naturalSort(i.name,h.name)});return g},_ensureIds:function(){this.initialList.forEach(function(g){if(!g.hasOwnProperty("id")){g.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(i){var h=[],g=[];this.unpaired.forEach(function(j){if(this._filterFwdFn(j)){h.push(j)}if(this._filterRevFn(j)){g.push(j)}}.bind(this));return[h,g]},_filterFwdFn:function(g){return g.name.indexOf(this.filters[0])>=0},_filterRevFn:function(g){return g.name.indexOf(this.filters[1])>=0},_addToUnpaired:function(h){var g=function(i,k){if(i===k){return i}var j=Math.floor((k-i)/2)+i,l=naturalSort(h.name,this.unpaired[j].name);if(l<0){return g(i,j)}else{if(l>0){return g(j+1,k)}}while(this.unpaired[j]&&this.unpaired[j].name===h.name){j++}return j}.bind(this);this.unpaired.splice(g(0,this.unpaired.length),0,h)},autoPair:function(g){g=g||this.strategy;this.simpleAutoPair();return this[g].call(this)},simpleAutoPair:function(){var m=0,k,q=this._splitByFilters(),g=q[0],p=q[1],o,r,h=false;while(m<g.length){var l=g[m];o=l.name.replace(this.filters[0],"");h=false;for(k=0;k<p.length;k++){var n=p[k];r=n.name.replace(this.filters[1],"");if(l!==n&&o===r){h=true;this._pair(g.splice(m,1)[0],p.splice(k,1)[0],{silent:true});break}}if(!h){m+=1}}},autoPairLevenshtein:function(){var n=0,l,s=this._splitByFilters(),g=s[0],q=s[1],p,u,h,r,k;while(n<g.length){var m=g[n];p=m.name.replace(this.filters[0],"");k=Number.MAX_VALUE;for(l=0;l<q.length;l++){var o=q[l];u=o.name.replace(this.filters[1],"");if(m!==o){if(p===u){r=l;k=0;break}h=d(p,u);if(h<k){r=l;k=h}}}var t=1-(k/(Math.max(p.length,u.length)));if(t>=this.matchPercentage){this._pair(g.splice(n,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{n+=1}}},autoPairLCSs:function(){var l=0,h,s=this._splitByFilters(),g=s[0],q=s[1],p,v,u,r,n;if(!g.length||!q.length){return}while(l<g.length){var k=g[l];p=k.name.replace(this.filters[0],"");n=0;for(h=0;h<q.length;h++){var o=q[h];v=o.name.replace(this.filters[1],"");if(k!==o){if(p===v){r=h;n=p.length;break}var m=this._naiveStartingAndEndingLCS(p,v);u=m.length;if(u>n){r=h;n=u}}}var t=n/(Math.min(p.length,v.length));if(t>=this.matchPercentage){this._pair(g.splice(l,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{l+=1}}},_naiveStartingAndEndingLCS:function(l,h){var m="",n="",k=0,g=0;while(k<l.length&&k<h.length){if(l[k]!==h[k]){break}m+=l[k];k+=1}if(k===l.length){return l}if(k===h.length){return h}k=(l.length-1);g=(h.length-1);while(k>=0&&g>=0){if(l[k]!==h[g]){break}n=[l[k],n].join("");k-=1;g-=1}return m+n},_pair:function(i,g,h){h=h||{};var j=this._createPair(i,g,h.name);this.paired.push(j);this.unpaired=_.without(this.unpaired,i,g);if(!h.silent){this.trigger("pair:new",j)}return j},_createPair:function(i,g,h){if(!(i&&g)||(i===g)){throw new Error("Bad pairing: "+[JSON.stringify(i),JSON.stringify(g)])}h=h||this._guessNameForPair(i,g);return{forward:i,name:h,reverse:g}},_guessNameForPair:function(i,g){var h=this._naiveStartingAndEndingLCS(i.name.replace(this.filters[0],""),g.name.replace(this.filters[1],""));return h||(i.name+" & "+g.name)},_unpair:function(h,g){g=g||{};if(!h){throw new Error("Bad pair: "+JSON.stringify(h))}this.paired=_.without(this.paired,h);this._addToUnpaired(h.forward);this._addToUnpaired(h.reverse);if(!g.silent){this.trigger("pair:unpair",[h])}return h},unpairAll:function(){var g=[];while(this.paired.length){g.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",g)},_pairToJSON:function(g){return{collection_type:"paired",src:"new_collection",name:g.name,element_identifiers:[{name:"forward",id:g.forward.id,src:"hda"},{name:"reverse",id:g.reverse.id,src:"hda"}]}},createList:function(){var i=this,h;if(i.historyId){h="/api/histories/"+this.historyId+"/contents/dataset_collections"}var g={type:"dataset_collection",collection_type:"list:paired",name:_.escape(i.$(".collection-name").val()),element_identifiers:i.paired.map(function(j){return i._pairToJSON(j)})};return jQuery.ajax(h,{type:"POST",contentType:"application/json",data:JSON.stringify(g)}).fail(function(m,j,l){console.error(m,j,l);var k=e("An error occurred while creating this collection");if(m){if(m.readyState===0&&m.status===0){k+=": "+e("Galaxy could not be reached and may be updating.")+e(" Try again in a few minutes.")}else{if(m.responseJSON){k+="<br /><pre>"+JSON.stringify(m.responseJSON)+"</pre>"}else{k+=": "+l}}}i._showAlert(k,"alert-danger")}).done(function(j,k,l){i.trigger("collection:created",j,k,l);if(typeof i.oncreate==="function"){i.oncreate.call(this,j,k,l)}})},render:function(g,h){this.$el.empty().addClass("collection-creator").html(f.templates.main());this._renderHeader(g);this._renderMiddle(g);this._renderFooter(g);this._addPluginComponents();return this},_renderHeader:function(h,i){var 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",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",e(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",e(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",e(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>.',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};function d(h,g){if(h.length===0){return g.length}if(g.length===0){return h.length}var k=[];var m;for(m=0;m<=g.length;m++){k[m]=[m]}var l;for(l=0;l<=h.length;l++){k[0][l]=l}for(m=1;m<=g.length;m++){for(l=1;l<=h.length;l++){if(g.charAt(m-1)===h.charAt(l-1)){k[m][l]=k[m-1][l-1]}else{k[m][l]=Math.min(k[m-1][l-1]+1,Math.min(k[m][l-1]+1,k[m-1][l]+1))}}}return k[g.length][h.length]}(function(){jQuery.fn.extend({hoverhighlight:function g(i,h){i=i||"body";if(!this.size()){return this}$(this).each(function(){var k=$(this),j=k.data("target");if(j){k.mouseover(function(l){$(j,i).css({background:h})}).mouseout(function(l){$(j).css({background:""})})}});return this}})}());var b=function c(i,g){g=_.defaults(g||{},{datasets:i,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var h=new f(g).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:h.$el,width:"80%",height:"700px",closing_events:true});return h};return{PairedCollectionCreator:f,pairedCollectionCreatorModal:b}}); \ No newline at end of file diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1360,13 +1360,20 @@ .toast-error{background-color:#bd362f} .toast-info{background-color:#2f96b4} .toast-warning{background-color:#f89406} -@media all and (max-width:240px){#toast-container>div{padding:8px 8px 8px 50px;width:11em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:241px) and (max-width:480px){#toast-container>div{padding:8px 8px 8px 50px;width:18em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:481px) and (max-width:768px){#toast-container>div{padding:15px 15px 15px 50px;width:25em}}.collection-creator{height:100%;display:flex;flex-direction:column;align-items:stretch;align-content:stretch;overflow:hidden;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none}.collection-creator ol,.collection-creator li{list-style:none;padding:0;margin:0} +@media all and (max-width:240px){#toast-container>div{padding:8px 8px 8px 50px;width:11em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:241px) and (max-width:480px){#toast-container>div{padding:8px 8px 8px 50px;width:18em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:481px) and (max-width:768px){#toast-container>div{padding:15px 15px 15px 50px;width:25em}}.collection-creator{height:100%;overflow:hidden;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none}.collection-creator ol,.collection-creator li{list-style:none;padding:0;margin:0} .collection-creator>*:not(.popover){padding:0px 8px 0px 8px} .collection-creator .btn{border-color:#BFBFBF} .collection-creator .vertically-spaced{margin-top:8px} .collection-creator .scroll-container{overflow:auto} .collection-creator .truncate{overflow:hidden;white-space:nowrap;text-overflow:ellipsis} .collection-creator .empty-message{color:grey;font-style:italic} +.collection-creator.flex-row-container,.collection-creator .flex-row-container,.collection-creator .flex-column-container{display:-webkit-box;display:-webkit-flex;display:flex;-webkit-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;align-content:stretch} +.collection-creator.flex-row-container,.collection-creator .flex-row-container{-webkit-flex-direction:column;flex-direction:column} +.collection-creator .flex-row{-webkit-flex:1 auto;flex:1 0 auto} +.collection-creator .flex-row.no-flex{-webkit-flex:0 auto;flex:0 0 auto} +.collection-creator .flex-column-container{-webkit-flex-direction:row;flex-direction:row} +.collection-creator .flex-column{-webkit-flex:1 auto;flex:1 1 auto} +.collection-creator .flex-column.no-flex{-webkit-flex:0 auto;flex:0 0 auto} .collection-creator .choose-filters .help{margin-bottom:2px;font-size:90%;color:grey} .collection-creator .choose-filters button{width:100%;margin-top:2px} .collection-creator .header .alert{display:none} @@ -1374,8 +1381,8 @@ .collection-creator .column-title{height:22px;line-height:22px;overflow:hidden}.collection-creator .column-title:hover{text-decoration:underline;cursor:pointer} .collection-creator .column-title .title{font-weight:bold} .collection-creator .column-title .title-info{color:grey}.collection-creator .column-title .title-info:before{content:' - '} -.collection-creator .paired-column{text-align:center;width:22%;flex:0 1 auto} -.collection-creator .header{flex:0 0 auto;padding-bottom:8px}.collection-creator .header .main-help{max-height:36px;margin-bottom:16px;overflow:hidden;padding:8px;background:#f8f8f8}.collection-creator .header .main-help .help-content i{cursor:help;border-bottom:1px dotted grey;font-style:normal} +.collection-creator .paired-column{text-align:center;width:22%} +.collection-creator .header{padding-bottom:8px}.collection-creator .header .main-help{max-height:36px;margin-bottom:16px;overflow:hidden;padding:8px;background:#f8f8f8}.collection-creator .header .main-help .help-content i{cursor:help;border-bottom:1px dotted grey;font-style:normal} .collection-creator .header .main-help .help-content ul,.collection-creator .header .main-help .help-content li{list-style:circle;margin-left:16px} .collection-creator .header .main-help .help-content p:first-child{overflow:hidden;white-space:nowrap;text-overflow:ellipsis} .collection-creator .header .main-help .help-content .less-help{display:inline-block;width:100%;text-align:right} @@ -1383,11 +1390,7 @@ .collection-creator .header .column-headers .column-header .unpaired-filter{width:100%}.collection-creator .header .column-headers .column-header .unpaired-filter .search-query{width:100%;height:22px} .collection-creator .header .paired-column a:not(:last-child){margin-right:8px} .collection-creator .header .reverse-column .column-title{text-align:right} -.collection-creator .row-flex-container{display:flex;flex-direction:row;align-items:stretch;align-content:stretch} -.collection-creator .flex-column{flex:1 1 auto} -.collection-creator .middle{flex:1 0 auto;display:flex;flex-direction:column;align-items:stretch;align-content:stretch} -.collection-creator .unpaired-columns,.collection-creator .paired-columns{flex:1 0 auto;height:0;border:1px solid lightgrey;border-radius:3px;border-width:1px 0 1px 0;overflow-y:auto;padding:4px} -.collection-creator .unpaired-columns{flex:1 0 auto} +.collection-creator .unpaired-columns,.collection-creator .paired-columns{height:0;border:1px solid lightgrey;border-width:1px 0 1px 0;padding:4px} .collection-creator .paired-columns{margin-bottom:8px} .collection-creator .column-datasets{list-style:none;overflow:hidden}.collection-creator .column-datasets .dataset{height:32px;margin-bottom:2px;border:1px solid lightgrey;border-radius:3px;padding:0 8px 0 8px;line-height:28px;cursor:pointer;overflow:hidden}.collection-creator .column-datasets .dataset:last-child{margin-bottom:4px} .collection-creator .unpaired-columns .dataset.unpaired{border-color:grey}.collection-creator .unpaired-columns .dataset.unpaired:hover{border-color:black} @@ -1402,7 +1405,7 @@ .collection-creator .paired-columns .paired-column .dataset.paired{border-radius:0;border-width:2px 0 2px 0}.collection-creator .paired-columns .paired-column .dataset.paired .dataset-name:hover{text-decoration:underline} .collection-creator .paired-columns .reverse-column .dataset.paired{margin-right:32px;border-radius:0 3px 3px 0;border-left-color:grey;border-left-width:1px}.collection-creator .paired-columns .reverse-column .dataset.paired:before{margin-right:8px;font-family:FontAwesome;content:'\f060'} .collection-creator .paired-columns .reverse-column .unpair-btn{float:right;margin-top:-34px;width:31px;height:32px;border-color:transparent;background:transparent;font-size:120%}.collection-creator .paired-columns .reverse-column .unpair-btn:hover{border-color:#BFBFBF;background:#DEDEDE} -.collection-creator .footer{flex:0 0 auto;padding-bottom:8px}.collection-creator .footer .collection-name-prompt.validation-warning:before{content:'(required)';margin-right:4px;color:red} +.collection-creator .footer{padding-bottom:8px}.collection-creator .footer .collection-name-prompt.validation-warning:before{content:'(required)';margin-right:4px;color:red} .collection-creator .footer .collection-name{width:50%}.collection-creator .footer .collection-name.validation-warning{border-color:red} .collection-creator .footer .other-options>*{display:none;margin-left:4px} .collection-creator .footer .collection-name-prompt{margin:5px 4px 0 0} diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/style/src/less/ui/paired-collection-creator.less --- a/static/style/src/less/ui/paired-collection-creator.less +++ b/static/style/src/less/ui/paired-collection-creator.less @@ -2,11 +2,6 @@ .collection-creator { height: 100%; - display: flex; - flex-direction: column; - align-items: stretch; - align-content: stretch; - overflow: hidden; -webkit-user-select: none; @@ -43,6 +38,49 @@ font-style: italic; } + // ------------------------------------------------------------------------ flex + &.flex-row-container, + .flex-row-container, + .flex-column-container { + display: -webkit-box; + display: -webkit-flex; + display: flex; + + -webkit-align-items: stretch; + align-items: stretch; + -webkit-align-content: stretch; + align-content: stretch; + } + + // a series of vertical elements that will expand to fill available space + &.flex-row-container, + .flex-row-container { + -webkit-flex-direction: column; + flex-direction: column; + } + .flex-row { + -webkit-flex: 1 auto; + flex: 1 0 auto; + } + .flex-row.no-flex { + -webkit-flex: 0 auto; + flex: 0 0 auto; + } + + // a series of horizontal elements that will expand to fill available space + .flex-column-container { + -webkit-flex-direction: row; + flex-direction: row; + } + .flex-column { + -webkit-flex: 1 auto; + flex: 1 1 auto; + } + .flex-column.no-flex { + -webkit-flex: 0 auto; + flex: 0 0 auto; + } + // ------------------------------------------------------------------------ sub-components .choose-filters { .help { @@ -87,12 +125,10 @@ text-align: center; // mess with these two to make center more/less priority width: 22%; - flex: 0 1 auto; } // ------------------------------------------------------------------------ header .header { - flex: 0 0 auto; padding-bottom: 8px; .main-help { @@ -151,45 +187,21 @@ } - // ------------------------------------------------------------------------ flex - .row-flex-container { - display: flex; - flex-direction: row; - align-items: stretch; - align-content: stretch; - } - .flex-column { - flex: 1 1 auto; - } - // ------------------------------------------------------------------------ middle .middle { - // highest flex count - will priority fill with this - flex: 1 0 auto; - - display: flex; - flex-direction: column; - align-items: stretch; - align-content: stretch; } .unpaired-columns, .paired-columns { - flex: 1 0 auto; // huh! - giving these any static height will pull them in height: 0; // NOT setting the above will give a full-height page border: 1px solid lightgrey; - border-radius: 3px; border-width: 1px 0 1px 0; - overflow-y: auto; + //overflow-y: auto; padding: 4px; } // ------------------------------------------------------------------------ unpaired - .unpaired-columns { - flex: 1 0 auto; - } - .paired-columns { margin-bottom: 8px; } @@ -337,9 +349,6 @@ // ------------------------------------------------------------------------ footer .footer { - flex: 0 0 auto; - padding-bottom: 8px; - .collection-name-prompt.validation-warning:before { //TODO: localize (somehow) content: '(required)'; @@ -361,5 +370,6 @@ .collection-name-prompt { margin: 5px 4px 0 0; } + padding-bottom: 8px; } } 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: guerler: Merge
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/476aa78a1b1a/ Changeset: 476aa78a1b1a User: guerler Date: 2014-06-24 21:00:13 Summary: Merge Affected #: 76 files 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 24 Jun '14

24 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a15c52999493/ Changeset: a15c52999493 Branch: stable User: guerler Date: 2014-06-24 19:38:13 Summary: Charts plugin update Affected #: 164 files diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/app.css --- a/config/plugins/visualizations/charts/static/app.css +++ b/config/plugins/visualizations/charts/static/app.css @@ -1,3 +1,20 @@ +.charts-tooltip { + position: absolute; + text-align: center; + padding: 3px 5px 3px 5px; + font: 12px sans-serif; + background: white; + border: 1px solid gray; + border-radius: 4px; + pointer-events: none; +} + +.charts-tooltip-first { + font-weight: bold; + text-align: left; + padding-right: 5px; +} + .charts-grid .item { padding: 5px; margin: 5px; @@ -17,6 +34,7 @@ .charts-grid .image { padding: 10px; width: 100px; + height: 86px; } .charts-grid .title { @@ -47,6 +65,7 @@ margin-left: 5px; top: -1px; font-size: 1.0em; + display: inline; } .charts-viewport .icon { @@ -63,5 +82,6 @@ .charts-viewport .charts-viewport-canvas { display: block; width:100%; + min-height: 100px; height: inherit; } \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -86,6 +86,22 @@ } }, + // get root path + chartPath: function(chart_type) { + // create path from id + var path = chart_type.split(/_(.+)/); + + // check path + if (path.length >= 2) { + // return path + return path[0] + '/' + path[1]; + } else { + // log status + console.debug('FAILED App:chartPath() - Invalid format: ' + chart_type); + } + return undefined; + }, + // execute command execute: function(options) { }, diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var 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t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{url:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img src="'+e.url+'"/>'}}),r=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return'<label class="'+e.cls+'"><b>'+e.title+"</b></label>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),a=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" 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r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a 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i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" 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Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw 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u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bar/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar 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onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input 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n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:s,Button:u,Icon:o,ButtonIcon:a,Input:h,Anchor:f,Message:l,Searchbox:c,Select:t,ButtonMenu:n,Modal:r,Textarea:p,Image:i,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){e.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){s.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var 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Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" 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n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa 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o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.chart.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_y:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the 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arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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arguments.length?(o=e,t.x(e),m):o},m.y=function(e){return arguments.length?(u=e,t.y(e),m):u},m.clipEdge=function(e){return arguments.length?(l=e,m):l},m.color=function(n){return arguments.length?(s=e.utils.getColor(n),t.color(s),m):s},m.interpolate=function(e){return arguments.length?(p=e,m):p},m.defined=function(e){return arguments.length?(a=e,m):a},m.isArea=function(e){return arguments.length?(f=d3.functor(e),m):f},m},e.models.lineChart=function(){function N(m){return m.each(function(m){var x=d3.select(this),C=this,k=(a||parseInt(x.style("width"))||960)-o.left-o.right,L=(f||parseInt(x.style("height"))||400)-o.top-o.bottom;N.update=function(){x.call(N)},N.container=this,b.disabled=m.map(function(e){return!!e.disabled});if(!w){var A;w={};for(A in b)b[A]instanceof Array?w[A]=b[A].slice(0):w[A]=b[A]}if(!m||!m.length||!m.filter(function(e){return e.values.length}).length){var O=x.selectAll(".nv-noData").data([E]);return O.enter().append("text").attr("class","nvd3 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t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return arguments.length?(l=e,C):l},C.showLegend=function(e){return arguments.length?(c=e,C):c},C.showXAxis=function(e){return arguments.length?(h=e,C):h},C.showYAxis=function(e){return arguments.length?(p=e,C):p},C.tooltip=function(e){return arguments.length?(m=e,C):m},C.tooltips=function(e){return arguments.length?(v=e,C):v},C.tooltipContent=function(e){return arguments.length?(m=e,C):m},C.state=function(e){return arguments.length?(b=e,C):b},C.defaultState=function(e){return arguments.length?(w=e,C):w},C.noData=function(e){return arguments.length?(E=e,C):E},C.transitionDuration=function(e){return arguments.length?(T=e,C):T},C},e.models.multiChart=function(){function C(e){return e.each(function(e){var u=d3.select(this),f=this;C.update=function(){u.call(C)},C.container=this;var 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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charts",zoomable:!0,keywords:"default small",showmaxmin:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/histogram/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{x_axis_label:{init:"Values"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_precision:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/scatter/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",query_limit:1e4,settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",query_limit:1e3,library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/forms/default.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/forms/default.js @@ -0,0 +1,252 @@ +define([], function() { + +return { + title : '', + category : '', + library : '', + tag : '', + keywords : '', + query_limit : 0, + settings : { + separator_x : { + title : 'X axis', + type : 'separator' + }, + x_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'X-axis', + placeholder : 'Axis label' + }, + x_axis_type : { + title : 'Axis value type', + info : 'Select the value type of the axis.', + type : 'select', + init : 'auto', + data : [ + { + label : '-- Do not show values --', + value : 'hide', + operations : { + hide : ['x_axis_precision'] + } + }, + { + label : 'Auto', + value : 'auto', + operations : { + hide : ['x_axis_precision'] + } + }, + { + label : 'Float', + value : 'f', + operations : { + show : ['x_axis_precision'] + } + }, + { + label : 'Exponent', + value : 'e', + operations : { + show : ['x_axis_precision'] + } + }, + { + label : 'Integer', + value : 'd', + operations : { + hide : ['x_axis_precision'] + } + }, + { + label : 'Percentage', + value : 'p', + operations : { + show : ['x_axis_precision'] + } + }, + { + label : 'SI-prefix', + value : 's', + operations : { + hide : ['x_axis_precision'] + } + } + ] + }, + x_axis_precision : { + title : 'Axis tick format', + info : 'Select the tick format for the axis.', + type : 'select', + init : '1', + data : [ + { + label : '0.00001', + value : '5' + }, + { + label : '0.0001', + value : '4' + }, + { + label : '0.001', + value : '3' + }, + { + label : '0.01', + value : '2' + }, + { + label : '0.1', + value : '1' + }, + { + label : '1', + value : '0' + } + ] + + }, + separator_y : { + title : 'Y axis', + type : 'separator' + }, + y_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'Y-axis', + placeholder : 'Axis label' + }, + y_axis_type : { + title : 'Axis value type', + info : 'Select the value type of the axis.', + type : 'select', + init : 'auto', + data : [ + { + label : '-- Do not show values --', + value : 'hide', + operations : { + hide : ['y_axis_precision'] + } + }, + { + label : 'Auto', + value : 'auto', + operations : { + hide : ['y_axis_precision'] + } + }, + { + label : 'Float', + value : 'f', + operations : { + show : ['y_axis_precision'] + } + }, + { + label : 'Exponent', + value : 'e', + operations : { + show : ['y_axis_precision'] + } + }, + { + label : 'Integer', + value : 'd', + operations : { + hide : ['y_axis_precision'] + } + }, + { + label : 'Percentage', + value : 'p', + operations : { + show : ['y_axis_precision'] + } + }, + { + label : 'SI-prefix', + value : 's', + operations : { + hide : ['y_axis_precision'] + } + } + ] + }, + y_axis_precision : { + title : 'Axis tick format', + info : 'Select the tick format for the axis.', + type : 'select', + init : '1', + data : [ + { + label : '0.00001', + value : '5' + }, + { + label : '0.0001', + value : '4' + }, + { + label : '0.001', + value : '3' + }, + { + label : '0.01', + value : '2' + }, + { + label : '0.1', + value : '1' + }, + { + label : '1', + value : '0' + } + ] + + }, + separator_legend : { + title : 'Others', + type : 'separator' + }, + show_legend : { + title : 'Show legend', + info : 'Would you like to add a legend?', + type : 'radiobutton', + init : 'true', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + }, + use_panels : { + title : 'Use multi-panels', + info : 'Would you like to separate your data into individual panels?', + type : 'radiobutton', + init : 'false', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + } + } +}; + +}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/config.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/config.js +++ /dev/null @@ -1,195 +0,0 @@ -define([], function() { - -return { - title : 'Heatmap', - category : 'Data processing (requires \'charts\' tool from Toolshed)', - library : '', - tag : 'div', - use_panels : true, - execute : 'heatmap', - - // columns - columns : { - row_label : { - title : 'Row labels', - is_label : true - }, - col_label : { - title : 'Column labels', - is_label : true - }, - value : { - title : 'Observations' - }, - }, - - // settings - settings: { - /*limit : { - title : 'Limit', - info : 'Which to ranked clusters would you like to visualize', - type : 'select', - init : '20', - data : [ - { - label : '20', - value : '20' - }, - { - label : '30', - value : '30' - }, - { - label : '40', - value : '40' - }, - { - label : '50', - value : '50' - }, - { - label : '60', - value : '60' - }, - { - label : '70', - value : '70' - }, - { - label : '80', - value : '80' - }, - { - label : '90', - value : '90' - }, - { - label : '100', - value : '100' - } - ] - },*/ - color_set : { - title : 'Color scheme', - info : 'Select a color scheme for your heatmap', - type : 'select', - init : 'ocean', - data : [ - { - label : 'Cold-to-Hot', - value : 'hot' - }, - { - label : 'Cool', - value : 'cool' - }, - { - label : 'Copper', - value : 'copper' - }, - { - label : 'Gebco', - value : 'gebco' - }, - { - label : 'Globe', - value : 'globe' - }, - { - label : 'Gray scale', - value : 'gray' - }, - { - label : 'Haxby', - value : 'haxby' - }, - { - label : 'Jet', - value : 'jet' - }, - { - label : 'No-Green', - value : 'no_green' - }, - { - label : 'Ocean', - value : 'ocean' - }, - { - label : 'Polar', - value : 'polar' - }, - { - label : 'Rainbow', - value : 'rainbow' - }, - { - label : 'Red-to-Green', - value : 'redgreen' - }, - { - label : 'Red-to-green (saturated)', - value : 'red2green' - }, - { - label : 'Relief', - value : 'relief' - }, - { - label : 'Seismograph', - value : 'seis' - }, - { - label : 'Sealand', - value : 'sealand' - }, - { - label : 'Split', - value : 'split' - }, - { - label : 'Topo', - value : 'topo' - }, - { - label : 'Wysiwyg', - value : 'wysiwyg' - } - ] - }, - - sorting : { - title : 'Sorting', - info : 'How should the columns be clustered?', - type : 'select', - init : 'hclust', - data : [ - { - label : 'Read from dataset', - value : 'hclust' - }, - { - label : 'Sort column and row labels', - value : 'byboth' - }, - { - label : 'Sort column labels', - value : 'bycolumns' - }, - { - label : 'Sort by rows', - value : 'byrow' - } - ] - } - }, - - // menu definition - menu : function() { - return { - color_set : this.settings.color_set - } - } -}; - -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js +++ /dev/null @@ -1,52 +0,0 @@ -// dependencies -define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin'], function(Utils, HeatmapPlugin) { - -// color palettes -var colorSets = { - seis: ['#AA0000', '#D00000', '#F70000', '#FF1D00', '#FF4400', '#FF6A00', '#FF9000', '#FFB700', '#FFDD00', '#FFFF00', '#FFFF00', '#FFFF00', '#BDFF0C', '#73FF1A', '#3FFA36', '#16F45A', '#00D08B', '#0087CD', '#0048FA', '#0024E3'], - - sealand: ['#8C66FF', '#6A66FF', '#6684FF', '#66A7FF', '#66CAFF', '#66ECFF', '#66FFF0', '#66FFCE', '#66FFAB', '#66FF88', '#66FF66', '#88FF66', '#ABFF66', '#CEFF66', '#FFEEA6', '#FFD3A6', '#FFB8A6', '#FFAAB0', '#FFB5CB', '#FFC0E1'], - - redgreen: ['#005824', '#1A693B', '#347B53', '#4F8D6B', '#699F83', '#83B09B', '#9EC2B3', '#B8D4CB', '#D2E6E3', '#EDF8FB', '#FFFFFF', '#F1EEF6', '#E6D3E1','#DBB9CD', '#D19EB9', '#C684A4', '#BB6990', '#B14F7C', '#A63467', '#9B1A53', '#91003F'], - - ocean: ['#000000', '#000209', '#000413', '#00061E', '#000728', '#000932', '#002650', '#00426E', '#005E8C', '#007AAA', '#0096C8', '#22A9C2', '#45BCBB', '#67CFB5', '#8AE2AE', '#ACF6A8', '#BCF8B9', '#CBF9CA', '#DBFBDC', '#EBFDED'], - - cool: ['#00FFFF', '#0DF2FF', '#19E6FF', '#26D9FF', '#33CCFF', '#3FBFFF', '#4CB3FF', '#59A6FF', '#6699FF', '#738CFF', '#7F7FFF', '#8C73FF', '#9966FF', '#A659FF', '#B24DFF', '#BF3FFF', '#CC33FF', '#D926FF', '#E619FF', '#F20DFF'], - - copper: ['#000000', '#100906', '#1F130D', '#301E13', '#40281A', '#50321F', '#603C26', '#70462D', '#805033', '#905A3A', '#A06440', '#B06E46', '#C0784D', '#D08253', '#E08C5A', '#F09660', '#FFA066', '#FFAA6D', '#FFB473', '#FFBE7A'], - - gebco: ['#00F0FF', '#00F0FF', '#00F0FF', '#23FFFF', '#23FFFF', '#23FFFF', '#5AFFFF', '#5AFFFF', '#5AFFFF', '#8CFFE6', '#8CFFE6', '#8CFFE6', '#A5FFD7', '#A5FFD7', '#A5FFD7', '#C3FFD7', '#C3FFD7', '#C3FFD7', '#D2FFD7', '#E6FFF0'], - - globe: ['#9900FF', '#9900FF', '#7722FF', '#5544FF', '#3366FF', '#1188FF', '#1BA4FF', '#51BAFF', '#86D0FF', '#BCE6FF', '#336600', '#F3CA89', '#D9A627', '#A49019', '#9F7B0D', '#996600', '#B27676', '#C2B0B0', '#E5E5E5', '#FFFFFF'], - - gray: ['#000000', '#0D0D0D', '#191919', '#262626', '#333333', '#3F3F3F', '#4C4C4C', '#595959', '#666666', '#737373', '#7F7F7F', '#8C8C8C', '#999999', '#A6A6A6', '#B2B2B2', '#BFBFBF', '#CCCCCC', '#D9D9D9', '#E6E6E6', '#F2F2F2'], - - haxby: ['#090079', '#280096', '#0009C8', '#0019D4', '#1A66F0', '#19AFFF', '#32BEFF', '#61E1F0', '#6AECE1', '#8AECAE', '#CDFFA2', '#DFF68D', '#F8D768', '#FFBD57', '#F4754B', '#FF5A5A', '#FF7C7C', '#F6B3AE', '#FFC4C4', '#FFECEC'], - - hot: ['#000000', '#220000', '#440000', '#660000', '#880000', '#AA0000', '#CC0000', '#EE0000', '#FF1100', '#FF3300', '#FF5500', '#FF7700', '#FF9900', '#FFBB00', '#FFDD00', '#FFFF00', '#FFFF33', '#FFFF66', '#FFFF99', '#FFFFCC'], - - jet: ['#00007F', '#0000B2', '#0000E5', '#0019FF', '#004DFF', '#007FFF', '#00B2FF', '#00E5FF', '#FFFFF2', '#FFFFD9', '#FFFFBF', '#FFFFA5', '#FFFF8C', '#FFE500', '#FFB300', '#FF7F00', '#FF4C00', '#FF1900', '#E50000', '#B20000'], - - no_green: ['#1F60FF', '#1F60FF', '#1F9FFF', '#1FBFFF', '#00CFFF', '#2AFFFF', '#2AFFFF', '#55FFFF', '#7FFFFF', '#AAFFFF', '#FFFF54', '#FFFF54', '#FFF000', '#FFBF00', '#FFA800', '#FF8A00', '#FF8A00', '#FF7000', '#FF4D00', '#FF0000'], - - polar: ['#0000FF', '#1919FF', '#3333FF', '#4C4CFF', '#6666FF', '#7F7FFF', '#9999FF', '#B2B2FF', '#CCCCFF', '#E6E6FF', '#FFFFFF', '#FFE5E5', '#FFCCCC', '#FFB2B2', '#FF9999', '#FF7F7F', '#FF6666', '#FF4C4C', '#FF3333', '#FF1A1A'], - - rainbow: ['#FF00FF', '#BF00FF', '#7F00FF', '#3F00FF', '#0000FF', '#003FFF', '#007FFF', '#00BFFF', '#00FFFF', '#00FFBF', '#00FF7F', '#00FF3F', '#00FF00', '#3FFF00', '#7FFF00', '#BFFF00', '#FFFF00', '#FFBF00', '#FF7F00', '#FF3F00'], - - red2green: ['#FF0000', '#FF1919', '#FF3333', '#FF4C4C', '#FF6666', '#FF7F7F', '#FF9999', '#FFB2B2', '#FFCCCC', '#FFE6E6', '#FFFFFF', '#E5FFE5', '#CCFFCC', '#B2FFB2', '#99FF99', '#7FFF7F', '#66FF66', '#4CFF4C', '#33FF33', '#1AFF1A'], - - relief: ['#000000', '#000413', '#000728', '#002650', '#005E8C', '#0096C8', '#45BCBB', '#8AE2AE', '#BCF8B9', '#DBFBDC', '#467832', '#887438', '#B19D48', '#DBC758', '#FAE769', '#FAEB7E', '#FCED93', '#FCF1A7', '#FCF6C1', '#FDFAE0'], - - split: ['#7F7FFF', '#6666E6', '#4D4DCC', '#3333B3', '#1A1A99', '#00007F', '#000066', '#00004D', '#000033', '#00001A', '#000000', '#1A0000', '#330000', '#4D0000', '#660000', '#7F0000', '#991A1A', '#B33333', '#CC4D4D', '#E66666'], - - topo: ['#C977D9', '#A18AE6', '#8AA2E6', '#8BD1E7', '#8AF3CF', '#85F38E', '#BDF385', '#EDE485', '#F0B086', '#DE9F8B', '#74A3B3', '#99CC70', '#DCD68E', '#EDDFAD', '#F7E8CA', '#FFF9F3', '#FFF9F6', '#FFFBF9', '#FFFCFA', '#FFFEFD'], - - wysiwyg: ['#3F003F', '#3F003F', '#3F00BF', '#003FFF', '#00A0FF', '#3FBFFF', '#3FBFFF', '#40E0FF', '#3FFFBF', '#3FFF3F', '#7FFF3F', '#BFFF3F', '#BFFF3F', '#FFE040', '#FFE040', '#FF6040', '#FF1F40', '#FF60C0', '#FFA0FF', '#FFA0FF'] -} - -// return -return { - colorSets: colorSets -} - -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js +++ /dev/null @@ -1,739 +0,0 @@ -// dependencies -define(['utils/utils'], -function(Utils) { - -// widget -return Backbone.View.extend( -{ - // number of columns and rows - colNumber: 0, - rowNumber: 0, - - // indices - rowIndex: [], - colIndex: [], - - // labels - rowLabel: [], - colLabel: [], - - // cell size - cellSize: 0, - - // font size - fontSize: 0, - - // color buckets - nColors: 0, - - // margins as cells - margin : { - top : 5, - right : 5, - bottom : 5, - left : 5 - }, - - // default settings - optionsDefault: { - title : '', - pace : 1000, - }, - - // initialize - initialize: function(options) { - // link this - var self = this; - - // load options - this.options = Utils.merge(options, this.optionsDefault) - - // check requirements - if (!this.options.data || !this.options.div || !this.options.colors) { - console.debug('FAILED - HeatMapPlugin::initialize() - Parameters (container and/or data and/or colors) missing.'); - return; - } - - // link data - this.data = this.options.data; - - // set element - this.setElement(this.options.div); - - // - // data indexing - // - - // labels (in alphabetical order) - this.rowLabel = []; - this.colLabel = []; - - // index (order from original dataset) - this.rowIndex = []; - this.colIndex = []; - - // unique keys (key indices are unique per label and indicate the labels rank in the alphabetical sorting) - this.colRank = {}; - this.rowRank = {}; - - // - // identify and parse labels - // - for (var i in this.data) { - var cell = this.data[i]; - - // add label to index list - var col_label = cell.col_label; - if (this.colRank[col_label] === undefined) { - this.colRank[col_label] = true; - this.colLabel.push(col_label); - this.colIndex.push(col_label); - } - var row_label = cell.row_label; - if (this.rowRank[row_label] === undefined) { - this.rowRank[row_label] = true; - this.rowLabel.push(row_label); - this.rowIndex.push(row_label); - } - } - - // - // sort labels and update rank dictionary - // - - // set sizes - this.rowNumber = this.rowLabel.length - this.colNumber = this.colLabel.length - - // sort labels alphabetical - this.rowLabel.sort(); - this.colLabel.sort(); - - // generate sorted key list for rows - for (var i in this.rowLabel) { - var row_label = this.rowLabel[i]; - var row = parseInt(i); - this.rowRank[row_label] = row; - } - - // generate sorted key list for columns - for (var i in this.colLabel) { - var col_label = this.colLabel[i]; - var col = parseInt(i); - this.colRank[col_label] = col; - } - - // - // parse indexing from rank dictionary to cells - // - - // min/max - this.max = undefined; - this.min = undefined - - // add indices to data - for (var i in this.data) { - // get cell data - var cell = this.data[i]; - - // add rank - cell.col = this.colRank[cell.col_label]; - cell.row = this.rowRank[cell.row_label]; - - // identify max/min values - if (this.min == undefined || this.min > cell.value) { - this.min = cell.value; - } - if (this.max == undefined || this.max < cell.value) { - this.max = cell.value; - } - } - - // - // translate original create cluster from order in original data - // - - // generate sorted key list for columns - for (var i in this.colIndex) { - this.colIndex[i] = this.colRank[this.colIndex[i]]; - } - // generate sorted key list for columns - for (var i in this.rowIndex) { - this.rowIndex[i] = this.rowRank[this.rowIndex[i]]; - } - - // middle - this.mid = (this.max + this.min) / 2; - - // - // set colors - // - - // identify buckets - this.nColors = this.options.colors.length; - - // color scale - this.colorScale = d3.scale.quantile() - .domain([this.min, this.mid, this.max]) - .range(this.options.colors); - - // - // add ui elements - // - // create tooltip - this.$tooltip = $(this._templateTooltip()); - this.$el.append(this.$tooltip); - - // - // finally draw the heatmap - // - this._build(); - - // catch window resize event - $(window).resize(function () { - self._build(); - }); - }, - - _build: function() { - // link this - var self = this; - - // container (full draw area) - this.widthContainer = this.$el.width(); - this.heightContainer = this.$el.height(); - - // get grid dimensions - this.width = this.widthContainer; - this.height = this.heightContainer; - - // calculate cell size - this.cellSize = Math.min(((this.height) / (this.rowNumber + this.margin.top + this.margin.bottom)), - (this.width / (this.colNumber + this.margin.left + this.margin.right))); - - // set font size - this.fontSize = Math.min(this.cellSize, 16); - - // set width/height for plugin - this.width = this.cellSize * this.colNumber; - this.height = this.cellSize * this.rowNumber; - - // get dimensions - var margin = this.options.margin; - var width = this.width; - var height = this.height; - - // reset svg - if (this.svg !== undefined) { - this.$el.find('svg').remove(); - } - - // add main group and translate - this.svg = d3.select(this.$el[0]).append('svg') - .append('g') - .attr('transform', 'translate(' + (this.widthContainer - width) / 2 + ',' + - (this.heightContainer - height) / 2 + ')'); - - // reset sorting - this.rowSortOrder = false; - this.colSortOrder = false; - - // build - this.d3RowLabels = this._buildRowLabels(); - this.d3ColLabels = this._buildColLabels(); - this.d3HeatMap = this._buildHeatMap(); - this.d3Legend = this._buildLegend(); - this.d3Title = this._buildTitle(); - }, - - // build title - _buildTitle: function() { - // link this - var self = this; - - // gather data - var height = this.height; - var width = this.width; - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var title = this.options.title; - - // add title - return this.svg.append('g') - .append('text') - .attr('x', width / 2) - .attr('y', height + 3 * cellSize + fontSize + 3) - .attr('text-anchor', 'middle') - .text(title); - }, - - // build legend - _buildLegend: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var height = this.height; - var legendCellWidth = this.width / this.nColors; - - // create range labels - var dataRange = []; - for(var i = 0; i < this.nColors; i++) { - dataRange.push(''); - } - - // prepare indices - var dataRangeMin = 0; - var dataRangeMid = parseInt((dataRange.length - 1) / 2); - var dataRangeMax = dataRange.length - 1; - - // add labels - dataRange[dataRangeMin] = this.min; - dataRange[dataRangeMid] = this.mid; - dataRange[dataRangeMax] = this.max; - - // create legend - var legend = this.svg.selectAll('.legend') - .data(dataRange) - .enter().append('g') - .attr('class', 'legend'); - - // add boxes - legend.append('rect') - .attr('x', function(d, i) { - return legendCellWidth * i; - }) - .attr('y', height + cellSize) - .attr('width', legendCellWidth) - .attr('height', cellSize) - .style('fill', function(d, i) { - return self.options.colors[i]; - }); - - // add text - legend.append('text') - .attr('class', 'mono') - .text(function(d) { - return d; - }) - .attr('width', legendCellWidth) - .attr('x', function(d, i) { - return legendCellWidth * i; - }) - .attr('y', height + cellSize - 3) - .style('font-size', fontSize + 'px'); - - // return - return legend; - }, - - // build column labels - _buildColLabels: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // column labels - var colLabels = this.svg.append('g') - .selectAll('.colLabelg') - .data(colLabel) - .enter() - .append('text') - .text(function (d) { - return d; - }) - .attr('x', 0) - .attr('y', function (d, i) { - return colIndex.indexOf(i) * cellSize; - }) - .style('font-size', fontSize + 'px') - .style('text-anchor', 'left') - .attr('transform', 'translate(' + cellSize / 2 + ', -17) rotate (-90)') - .attr('class', function (d, i) { - return 'colLabel mono c' + i; - }) - .on('mouseover', function(d) { - d3.select(this).classed('text-hover',true); - }) - .on('mouseout' , function(d) { - d3.select(this).classed('text-hover',false); - }) - .on('click', function(d, i) { - self.colSortOrder=!self.colSortOrder; - self._sortByLabel('c', 'row', self.rowNumber, i, self.colSortOrder); - d3.select('#order').property('selectedIndex', 4).node().focus(); - }); - - // return - return colLabels; - }, - - // build row labels - _buildRowLabels: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var fontSize = this.fontSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - - // draw labels - var rowLabels = this.svg.append('g') - .selectAll('.rowLabelg') - .data(rowLabel) - .enter() - .append('text') - .text(function (d) { - return d; - }) - .attr('x', 0) - .attr('y', function (d, i) { - return rowIndex.indexOf(i) * cellSize; - }) - .style('font-size', fontSize + 'px') - .style('text-anchor', 'end') - .attr('transform', 'translate(-10,' + cellSize / 1.5 + ')') - .attr('class', function (d, i) { - return 'rowLabel mono r' + i; - } ) - .on('mouseover', function(d) { - d3.select(this).classed('text-hover',true); - }) - .on('mouseout' , function(d) { - d3.select(this).classed('text-hover',false); - }) - .on('click', function(d, i) { - self.rowSortOrder=!self.rowSortOrder; - self._sortByLabel('r', 'col', self.colNumber, i, self.rowSortOrder); - d3.select('#order').property('selectedIndex', 4).node().focus(); - }); - - // return - return rowLabels; - }, - - // build heat map - _buildHeatMap: function() { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // heat map - var heatmap = this.svg.append('g').attr('class','g3') - .selectAll('.cellg') - .data(self.data, function(d) { - return d.row + ':' + d.col; - }) - .enter() - .append('rect') - .attr('x', function(d) { - return colIndex.indexOf(d.col) * cellSize; - }) - .attr('y', function(d) { - return rowIndex.indexOf(d.row) * cellSize; - }) - .attr('class', function(d){ - return 'cell cell-border cr' + d.row + ' cc' + d.col; - }) - .attr('width', cellSize) - .attr('height', cellSize) - .style('fill', function(d) { - return self.colorScale(d.value); - }) - .on('mouseover', function(d){ - // highlight text - d3.select(this).classed('cell-hover',true); - d3.selectAll('.rowLabel').classed('text-highlight',function(r,ri){ return ri==(d.row);}); - d3.selectAll('.colLabel').classed('text-highlight',function(c,ci){ return ci==(d.col);}); - - // update the tooltip position and value - d3.select('#heatmap-tooltip') - .style('left', (d3.event.pageX+10) + 'px') - .style('top', (d3.event.pageY-10) + 'px') - .select('#value') - .text('Label: ' + rowLabel[d.row] + ' | ' + colLabel[d.col] + ', Value: ' + d.value); - // show the tooltip - d3.select('#heatmap-tooltip').classed('hidden', false); - }) - .on('mouseout', function(){ - d3.select(this).classed('cell-hover',false); - d3.selectAll('.rowLabel').classed('text-highlight',false); - d3.selectAll('.colLabel').classed('text-highlight',false); - d3.select('#heatmap-tooltip').classed('hidden', true); - }); - - // return - return heatmap; - }, - - // change ordering of cells - _sortByLabel: function(rORc, rowORcol, n, index, sortOrder) { - // get cell size - var cellSize = this.cellSize; - - // define transition / prepare element - var t = this.svg.transition().duration(this.options.pace); - - // create cells - var cells=[]; - for (var i = 0; i < n; i++) { - cells[i] = { - value: this.min - 1 - } - cells[i][rowORcol] = i; - } - - // collect cells - t.selectAll('.c' + rORc + index).filter(function(ce) { - cells[ce[rowORcol]].value = ce.value; - }); - - // sort cells - cells.sort(function(a, b) { - if (sortOrder) { - return b.value - a.value; - } else { - return a.value - b.value; - } - }); - - // get sorted key list - var sorted = []; - for (var i in cells) { - sorted.push(cells[i][rowORcol]); - } - - // rows or columns - if(rORc == 'r') { - // sort cells - t.selectAll('.cell') - .attr('x', function(d) { - return sorted.indexOf(d.col) * cellSize; - }); - - // sort labels - t.selectAll('.colLabel') - .attr('y', function (d, i) { - return sorted.indexOf(i) * cellSize; - }); - } else { - // sort cells - t.selectAll('.cell') - .attr('y', function(d) { - return sorted.indexOf(d.row) * cellSize; - }); - - // sort labels - t.selectAll('.rowLabel') - .attr('y', function (d, i) { - return sorted.indexOf(i) * cellSize; - }); - } - }, - - // sort function - _sortByOrder: function (value) { - // link this - var self = this; - - // gather data - var cellSize = this.cellSize; - var rowIndex = this.rowIndex; - var rowLabel = this.rowLabel; - var colIndex = this.colIndex; - var colLabel = this.colLabel; - - // set duration / select element - var t = this.svg.transition().duration(this.options.pace); - if(value=='hclust'){ - t.selectAll('.cell') - .attr('x', function(d) { - return colIndex.indexOf(d.col) * cellSize; - }) - .attr('y', function(d) { - return rowIndex.indexOf(d.row) * cellSize; - }); - - t.selectAll('.rowLabel') - .attr('y', function(d, i) { - return rowIndex.indexOf(i) * cellSize; - }); - - t.selectAll('.colLabel') - .attr('y', function(d, i) { - return colIndex.indexOf(i) * cellSize; - }); - - } else if (value=='byboth') { - t.selectAll('.cell') - .attr('x', function(d) { - return d.col * cellSize; - }) - .attr('y', function(d) { - return d.row * cellSize; - }); - - t.selectAll('.rowLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - - t.selectAll('.colLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - } else if (value=='byrow') { - t.selectAll('.cell') - .attr('y', function(d) { - return d.row * cellSize; - }); - - t.selectAll('.rowLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - } else if (value=='bycol'){ - t.selectAll('.cell') - .attr('x', function(d) { - return d.col * cellSize; - }); - t.selectAll('.colLabel') - .attr('y', function (d, i) { - return i * cellSize; - }); - } - }, - - // selection of cells - _addSelectionTool: function() { - // - // selection - // - var sa=d3.select('.g3') - .on('mousedown', function() { - if( !d3.event.altKey) { - d3.selectAll('.cell-selected').classed('cell-selected', false); - d3.selectAll('.rowLabel').classed('text-selected', false); - d3.selectAll('.colLabel').classed('text-selected', false); - } - var p = d3.mouse(this); - sa.append('rect') - .attr({ - rx : 0, - ry : 0, - class : 'selection', - x : p[0], - y : p[1], - width : 1, - height : 1 - }) - }) - .on('mousemove', function() { - var s = sa.select('rect.selection'); - - if(!s.empty()) { - var p = d3.mouse(this), - d = { - x : parseInt(s.attr('x'), 10), - y : parseInt(s.attr('y'), 10), - width : parseInt(s.attr('width'), 10), - height : parseInt(s.attr('height'), 10) - }, - move = { - x : p[0] - d.x, - y : p[1] - d.y - }; - - if(move.x < 1 || (move.x*2<d.width)) { - d.x = p[0]; - d.width -= move.x; - } else { - d.width = move.x; - } - - if(move.y < 1 || (move.y*2<d.height)) { - d.y = p[1]; - d.height -= move.y; - } else { - d.height = move.y; - } - s.attr(d); - - // deselect all temporary selected state objects - d3.selectAll('.cell-selection.cell-selected').classed('cell-selected', false); - d3.selectAll('.text-selection.text-selected').classed('text-selected',false); - d3.selectAll('.cell').filter(function(cell_d, i) { - if(!d3.select(this).classed('cell-selected') && - // inner circle inside selection frame - (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width && - (this.y.baseVal.value)+cellSize >= d.y && (this.y.baseVal.value)<=d.y+d.height) - { - d3.select(this) - .classed('cell-selection', true) - .classed('cell-selected', true); - - d3.select('.r' + cell_d.row) - .classed('text-selection',true) - .classed('text-selected',true); - - d3.select('.c' + cell_d.col) - .classed('text-selection',true) - .classed('text-selected',true); - } - }); - } - }) - .on('mouseup', function() { - // remove selection frame - sa.selectAll('rect.selection').remove(); - - // remove temporary selection marker class - d3.selectAll('.cell-selection').classed('cell-selection', false); - d3.selectAll('.text-selection').classed('text-selection', false); - }) - .on('mouseout', function() { - if(d3.event.relatedTarget.tagName=='html') { - // remove selection frame - sa.selectAll('rect.selection').remove(); - - // remove temporary selection marker class - d3.selectAll('.cell-selection').classed('cell-selection', false); - d3.selectAll('.rowLabel').classed('text-selected',false); - d3.selectAll('.colLabel').classed('text-selected',false); - } - }); - }, - - // template - _templateSelect: function() { - return '<select id="order">' + - '<option value="hclust">Cluster</option>' + - '<option value="byboth">Sort by row and column</option>' + - '<option value="byrow">Sort by row label</option>' + - '<option value="bycol">Sort by column label</option>' + - '</select>'; - }, - - // template - _templateTooltip: function() { - return '<div id="heatmap-tooltip" class="hidden">' + - '<p><span id="value"></p>' - '</div>'; - } -}); -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/logo.png Binary file config/plugins/visualizations/charts/static/charts/heatmap/logo.png has changed diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js +++ /dev/null @@ -1,86 +0,0 @@ -// dependencies -define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin', 'plugin/charts/heatmap/heatmap-parameters'], -function(Utils, HeatmapPlugin, HeatmapParameters) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - // link this - var self = this; - - // loop through data groups - var index = 0; - for (var group_index in request_dictionary.groups) { - - // configure request - var tmp_dict = { - id : request_dictionary.id, - groups : [{ - key : request_dictionary.groups[group_index].key, - columns : { - row_label: { - index : index++, - is_label : true - }, - col_label: { - index : index++, - is_label : true - }, - value: { - index : index++ - } - } - }] - }; - - // target div - var group_div = self.options.canvas[group_index]; - - // draw group - this._draw_group(group_index, group_div, chart, tmp_dict, function(group_index) { - if (group_index == request_dictionary.groups.length - 1) { - // set chart state - chart.state('ok', 'Heat map drawn.'); - - // unregister process - chart.deferred.done(process_id); - } - }); - } - }, - - // draw group - _draw_group: function(group_index, div, chart, request_dictionary, callback) { - // link this - var self = this; - - // request data - this.app.datasets.request(request_dictionary, function() { - - // get group - var group = request_dictionary.groups[0]; - - // draw plot - var heatmap = new HeatmapPlugin({ - 'title' : group.key, - 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')], - 'data' : group.values, - 'div' : div - }); - - // callback on completion - callback (group_index); - }); - } -}); - -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js --- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js +++ /dev/null @@ -1,40 +0,0 @@ -define([], function() { - -return { - title : 'Box plot', - category : 'Data processing (requires \'charts\' tool from Toolshed)', - library : 'highcharts.js', - tag : 'div', - execute : 'boxplot', - columns : { - y : { - title : 'Observations' - } - }, - settings : { - separator_label : { - title : 'X axis', - type : 'separator' - }, - x_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'X-axis', - placeholder : 'Axis label' - }, - separator_tick : { - title : 'Y axis', - type : 'separator' - }, - y_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'Y-axis', - placeholder : 'Axis label' - } - } -}; - -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png Binary file config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png has changed diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js +++ /dev/null @@ -1,122 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -// widget -return Backbone.View.extend( -{ - // highcharts configuration - hc_config : { - chart: { - type: 'boxplot' - }, - - title: { - text: '' - }, - - legend: { - enabled: false - }, - - credits: { - enabled: false - }, - - plotOptions: { - series: { - animation: false - } - }, - - xAxis: { - categories: [], - title: { - text: '' - } - }, - - yAxis: { - title: { - text: '' - } - }, - - series: [{ - name: 'Details:', - data: [], - tooltip: { - headerFormat: '<em>{point.key}</em><br/>' - } - }] - }, - - // initialize - initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { - // configure request - var index = 0; - for (var i in request_dictionary.groups) { - var group = request_dictionary.groups[i]; - group.columns = null; - group.columns = { - x: { - index: index++ - } - } - } - - // set axis labels - this.hc_config.xAxis.title.text = chart.settings.get('x_axis_label'); - this.hc_config.yAxis.title.text = chart.settings.get('y_axis_label'); - - // request data - var self = this; - this.app.datasets.request(request_dictionary, function() { - - // reset data/categories - var data = []; - var categories = []; - - // loop through data groups - for (var key in request_dictionary.groups) { - // get group - var group = request_dictionary.groups[key]; - - // add category - categories.push(group.key); - - // format chart data - var point = []; - for (var key in group.values) { - point.push(group.values[key].x); - } - - // add to data - data.push (point); - } - - // categories - self.hc_config.xAxis.categories = categories; - - // update data - self.hc_config.series[0].data = data; - - // draw plot - self.options.canvas[0].highcharts(self.hc_config); - - // set chart state - chart.state('ok', 'Box plot drawn.'); - - // unregister process - chart.deferred.done(process_id); - }); - } -}); - -}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js @@ -0,0 +1,20 @@ +define(['plugin/charts/jqplot/common/config'], function(plot_config) { + +return $.extend(true, {}, plot_config, { + title : 'Regular', + category : 'Bar diagrams', + columns : { + x : { + title : 'Values for x-axis', + is_label : true, + is_auto : true, + is_unique : true + }, + y : { + title : 'Values for y-axis', + is_numeric : true + } + } +}); + +}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png Binary file config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png has changed diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js @@ -0,0 +1,26 @@ +// dependencies +define(['plugin/charts/jqplot/common/wrapper'], function(Plot) { + +// widget +return Backbone.Model.extend({ + initialize: function(app, options) { + options.makeConfig = function(groups, plot_config){ + $.extend(true, plot_config, { + seriesDefaults: { + renderer : $.jqplot.BarRenderer + }, + axes: { + xaxis: { + min : -1 + }, + yaxis: { + pad : 1.2 + } + } + }); + }; + new Plot(app, options); + } +}); + +}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js @@ -0,0 +1,23 @@ +define(['plugin/charts/jqplot/common/config'], function(plot_config) { + +return $.extend(true, {}, plot_config, { + title : 'Box plot', + category : 'Data processing (requires \'charts\' tool from Toolshed)', + library : 'jqPlot', + tag : 'div', + execute : 'boxplot', + keywords : 'small medium large', + columns : { + y : { + title : 'Observations', + is_numeric : true + } + }, + settings : { + show_legend : { + init : 'false' + } + } +}); + +}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png Binary file config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png has changed diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js @@ -0,0 +1,127 @@ +// dependencies +define(['plugin/charts/jqplot/common/wrapper', 'plugin/charts/tools'], function(Plot, Tools) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + // get request dictionary + var request_dictionary = options.request_dictionary; + var chart = options.chart; + + // modify request + var index = 0; + for (var i in request_dictionary.groups) { + var group = request_dictionary.groups[i]; + group.columns = null; + group.columns = { + x: { + index: index++ + } + } + } + + // create plot + var plot = new Plot(app, { + process_id : options.process_id, + chart : options.chart, + request_dictionary : options.request_dictionary, + canvas_list : options.canvas_list, + makeConfig : function(groups, plot_config){ + var boundary = Tools.getDomains(groups, 'x'); + $.extend(true, plot_config, { + seriesDefaults: { + renderer: $.jqplot.OHLCRenderer, + rendererOptions : { + candleStick : true, + fillUpBody : true, + fillDownBody : true + } + }, + axes : { + xaxis: { + min: -1, + max: groups.length + 0.01 + }, + yaxis: { + min: boundary.x.min, + max: boundary.x.max + } + } + }); + }, + makeCategories: function(groups) { + // define custom category labels + var x_labels = []; + for (var group_index in groups) { + x_labels.push(groups[group_index].key); + } + + // use default mapping + Tools.mapCategories (groups, x_labels); + + // return labels array for x axis + return { + array: { + x : x_labels + } + } + }, + makeSeriesLabels : function (groups, plot_config) { + return [{ + label: 'Boxplot values' + }]; + }, + makeSeries: function (groups) { + /*/ example data + var catOHLC = [ + [0, 138.7, 139.68, 135.18, 135.4], + [1, 143.46, 144.66, 139.79, 140.02], + [2, 140.67, 143.56, 132.88, 142.44], + [3, 136.01, 139.5, 134.53, 139.48] + ]; + return [catOHLC];*/ + + // plot data + var plot_data = []; + + // check group length + if (groups.length == 0 || groups[0].values.length < 5) { + chart.state('failed', 'Boxplot data could not be found.'); + return [plot_data]; + } + + // loop through data groups + var indeces = [2, 4, 0, 1]; + for (var group_index in groups) { + // get group + var group = groups[group_index]; + + // format chart data + var point = []; + point.push(parseInt(group_index)); + for (var key in indeces) { + point.push(group.values[indeces[key]].x); + } + + // add to data + plot_data.push (point); + } + + // HACK: the boxplot renderer has an issue with single elements + var point = []; + point[0] = plot_data.length; + for (var key in indeces) { + point.push(0); + } + plot_data.push (point); + + // return + return [plot_data]; + } + }); + } +}); + +}); \ No newline at end of file diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/common/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js @@ -0,0 +1,51 @@ +define(['plugin/charts/forms/default'], function(config_default) { + +return $.extend(true, {}, config_default, { + title : '', + category : '', + library : 'jqPlot', + tag : 'div', + zoomable : true, + keywords : 'medium', + query_limit : 10000, + settings : { + separator_grid : { + title : 'Grids', + type : 'separator' + }, + x_axis_grid : { + title : 'Axis grid', + info : 'Would you like to show grid lines for the X axis?', + type : 'radiobutton', + init : 'false', + data : [ + { + label : 'On', + value : 'true' + }, + { + label : 'Off', + value : 'false' + } + ] + }, + y_axis_grid : { + title : 'Axis grid', + info : 'Would you like to show grid lines for the Y axis?', + type : 'radiobutton', + init : 'true', + data : [ + { + label : 'On', + value : 'true' + }, + { + label : 'Off', + value : 'false' + } + ] + } + } +}); + +}); \ No newline at end of file This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/8bf883f2638e/ Changeset: 8bf883f2638e Branch: stable User: guerler Date: 2014-06-24 19:50:03 Summary: Charts style update Affected #: 2 files diff -r a15c52999493cd723c114899d4224912b2c28ffc -r 8bf883f2638e1bae7a1761a0fab98a981d6fa315 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -148,7 +148,7 @@ .form-control::-moz-placeholder{color:#999} .form-control:-ms-input-placeholder{color:#999} .form-control::-webkit-input-placeholder{color:#999} -.form-control{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} +.form-control,.ui-input{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} .form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee} textarea.form-control{height:auto} .form-group{margin-bottom:15px} @@ -1278,17 +1278,25 @@ .upload-ftp .upload-ftp-help{margin-bottom:10px} .upload-ftp .upload-ftp-warning{text-align:center;margin-top:20px} .upload-settings .upload-settings-cover{position:absolute;width:100%;height:100%;top:0px;left:0px;background:#fff;opacity:0.4;cursor:no-drop} +.ui-radiobutton label{height:23px;line-height:1em} +.ui-table-form-separator{font-weight:bold;font-size:0.9em} +.ui-label{font-weight:bold} +.ui-message{padding:2px 2px 2px 10px} +.ui-icon{font-size:1.2em} +.ui-button-icon{margin-right:5px}.ui-button-icon ul i{font-size:1.2em;margin-right:5px;position:relative;top:1px} +.ui-button-icon .button{margin-right:5px;margin-left:5px} +.ui-button-icon .title{position:relative;font-size:0.8em;font-weight:normal;top:-1px} +.ui-tabs .ui-tabs-add{font-size:0.8em;margin-right:5px} +.ui-tabs .ui-tabs-delete{font-size:0.8em;margin-left:5px;cursor:pointer} .no-highlight{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} -.portlet-view{min-width:300px}.portlet-view .portlet-title-icon{float:left;font-size:1.2em;padding-top:4px} -.portlet-view .portlet-title{overflow:hidden;padding:2px 5px 2px 10px} -.portlet-view .portlet-title-text{float:left;padding-top:2px} -.portlet-view .portlet-operations{float:right;cursor:pointer} -.portlet-view .portlet-buttons{height:50px;padding:10px} -.portlet-view .portlet-content{height:inherit;padding:10px} -.popover-view{max-width:700px;display:none}.popover-view .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer} -.popover-view .popover-title{padding:4px 10px} -.styled-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.styled-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2} -.styled-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none} +.ui-portlet{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header{padding:5px 10px;background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header h1,.ui-portlet .portlet-header h2,.ui-portlet .portlet-header h3,.ui-portlet .portlet-header h4,.ui-portlet .portlet-header h5,.ui-portlet .portlet-header h6{float:left;font-weight:normal;display:inline-block;vertical-align:middle;font-size:1em;margin:3px}.ui-portlet .portlet-header h1 .icon,.ui-portlet .portlet-header h2 .icon,.ui-portlet .portlet-header h3 .icon,.ui-portlet .portlet-header h4 .icon,.ui-portlet .portlet-header h5 .icon,.ui-portlet .portlet-header h6 .icon{font-size:1.2em} +.ui-portlet .portlet-buttons{height:50px;padding:10px} +.ui-portlet .portlet-content{height:inherit;padding:10px;clear:both}.ui-portlet .portlet-content .content{padding:10px;height:100%;width:100%}.ui-portlet .portlet-content .content .buttons{height:50px;padding:10px} +.ui-portlet .no-scroll{height:calc(100% - 80px)} +.ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer} +.ui-popover .popover-title{padding:4px 10px} +.ui-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.ui-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2} +.ui-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none} .libraryRow{background-color:#ebd9b2} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} @@ -1453,7 +1461,7 @@ div.form-row-input{width:90%;float:left} div.form-row-input label{font-weight:normal;display:inline} div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0} -.form-row .help,.toolParamHelp{color:#666}.form-row .help a,.toolParamHelp a{color:#666} +.form-row .help,.toolParamHelp,.ui-table-form-info{color:#666}.form-row .help a,.toolParamHelp a{color:#666} .form-row.form-actions{background:whiteSmoke;border-top:solid #ddd 1px;padding-top:10px;padding-bottom:10px;margin-top:5px} select{padding:2px;font-size:12px;line-height:1.428571429} select,input,textarea{font:inherit} @@ -1519,13 +1527,13 @@ .grid-header{padding-bottom:1em} .grid-header h2{margin:0;margin-bottom:0.5em} .grid-header .title{font-weight:bold} -.grid{padding-top:1em;border-collapse:collapse;width:100%} -.grid tbody td{line-height:1.428571429;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px} +.grid,.ui-table{padding-top:1em;border-collapse:collapse;width:100%} +.grid tbody td,.ui-table tbody td{line-height:1.428571429;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px} .grid tbody td:empty{padding:0} .grid thead tr{height:2em} .grid thead th{line-height:1.428571429;background:#ebd9b2;color:#000;border-top:solid #d6b161 1px;border-bottom:solid #d6b161 1px;padding:5px;text-align:left;white-space:nowrap} .grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px} -.grid .current{background-color:#EEEEFF} +.grid .current,.ui-table .current{background-color:#EEEEFF} .count-box{min-width:1.1em;padding:5px;border-width:1px;border-style:solid;text-align:center;display:inline-block} .text-filter-val{border:solid 1px #AAAAAA;padding:1px 2px 1px 3px;margin-right:5px;-moz-border-radius:.5em;-webkit-border-radius:.5em;font-style:italic} .page-link a,.inactive-link{padding:0px 7px 0px 7px;color:#555} diff -r a15c52999493cd723c114899d4224912b2c28ffc -r 8bf883f2638e1bae7a1761a0fab98a981d6fa315 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -1,3 +1,80 @@ +.ui-radiobutton { + label { + height: 23px; + line-height: 1em; + } +} + +.ui-table { + &:extend(.grid); + + tbody td { + &:extend(.grid tbody td); + } + .current { + &:extend(.grid .current); + } +} + +.ui-table-form-info { + &:extend(.toolParamHelp); +} + +.ui-table-form-separator { + font-weight: bold; + font-size: 0.9em; +} + +.ui-label { + font-weight: bold; +} + +.ui-message { + padding: 2px 2px 2px 10px; +} + +.ui-icon { + font-size: 1.2em; +} + +.ui-button-icon { + margin-right: 5px; + ul { + i { + font-size: 1.2em; margin-right: 5px; position: relative; top: 1px; + } + } +} + +.ui-button-icon .button { + margin-right: 5px; + margin-left: 5px; +} + +.ui-button-icon .title { + position: relative; + font-size: 0.8em; + font-weight: normal; + top: -1px; +} + +.ui-input { + &:extend(.form-control); +} + +.ui-tabs { + .ui-tabs-add { + font-size : 0.8em; + margin-right : 5px; + } + + .ui-tabs-delete { + font-size : 0.8em; + margin-left : 5px; + cursor : pointer; + } +} + .no-highlight { -webkit-user-select: none; /* webkit (safari, chrome) browsers */ -moz-user-select: none; /* mozilla browsers */ @@ -5,30 +82,38 @@ -ms-user-select: none; /* IE10+ */ } -.portlet-view { - min-width: 300px; +.ui-portlet { + border: solid @form-border 1px; + .border-radius(@panel-border-radius); - .portlet-title-icon { - float: left; - font-size: 1.2em; - padding-top: 4px; - } - - .portlet-title { - overflow: hidden; - padding: 2px 5px 2px 10px; + position: relative; + clear: both; + width: auto; + height: 100%; + + .portlet-header { + padding: 5px 10px; + background: @form-heading-bg; + border-bottom: solid @form-border 1px; + padding: 2px 8px; + overflow: visible; + float: right; + width:100%; + + h1, h2, h3, h4, h5, h6 { + float: left; + font-weight: normal; + display: inline-block; + vertical-align: middle; + font-size: 1em; + margin: 3px; + + .icon { + font-size: 1.2em; + } + } } - .portlet-title-text { - float: left; - padding-top: 2px; - } - - .portlet-operations { - float: right; - cursor: pointer; - } - .portlet-buttons { height: 50px; padding: 10px; @@ -37,10 +122,26 @@ .portlet-content { height: inherit; padding: 10px; + clear: both; + + .content { + padding : 10px; + height : 100%; + width : 100%; + + .buttons { + height: 50px; + padding: 10px; + } + } + } + + .no-scroll { + height: ~'calc(100% - 80px)'; } } -.popover-view { +.ui-popover { max-width: 700px; display: none; @@ -57,7 +158,7 @@ } } -.styled-select { +.ui-select { position: relative; height: 27px; overflow: hidden; 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: Handle exporting and importing repository capsules with new ExportRepositoryManager and ImportRepositoryMnager classes respectively.
by commits-noreply＠bitbucket.org 24 Jun '14

24 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fdaad2cad392/ Changeset: fdaad2cad392 User: greg Date: 2014-06-24 19:11:24 Summary: Handle exporting and importing repository capsules with new ExportRepositoryManager and ImportRepositoryMnager classes respectively. Affected #: 10 files diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -10,14 +10,14 @@ from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import HTTPBadRequest from galaxy.web.framework.helpers import time_ago +from tool_shed.capsule import capsule_manager import tool_shed.repository_types.util as rt_util -import tool_shed.util.shed_util_common as suc from tool_shed.util import basic_util from tool_shed.util import encoding_util from tool_shed.util import hg_util -from tool_shed.util import import_util from tool_shed.util import metadata_util from tool_shed.util import repository_maintenance_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util log = logging.getLogger( __name__ ) @@ -248,10 +248,14 @@ except tarfile.ReadError, e: log.debug( 'Error opening capsule file %s: %s' % ( str( capsule_file_name ), str( e ) ) ) return {} + irm = capsule_manager.ImportRepositoryManager( trans.app, + trans.request.host, + trans.user, + trans.user_is_admin() ) capsule_dict[ 'tar_archive' ] = tar_archive capsule_dict[ 'capsule_file_name' ] = capsule_file_name - capsule_dict = import_util.extract_capsule_files( **capsule_dict ) - capsule_dict = import_util.validate_capsule( **capsule_dict ) + capsule_dict = irm.extract_capsule_files( **capsule_dict ) + capsule_dict = irm.validate_capsule( **capsule_dict ) status = capsule_dict.get( 'status', 'error' ) if status == 'error': log.debug( 'The capsule contents are invalid and cannot be imported:<br/>%s' % \ @@ -263,15 +267,12 @@ return {} file_path = encoding_util.tool_shed_decode( encoded_file_path ) export_info_file_path = os.path.join( file_path, 'export_info.xml' ) - export_info_dict = import_util.get_export_info_dict( export_info_file_path ) + export_info_dict = irm.get_export_info_dict( export_info_file_path ) manifest_file_path = os.path.join( file_path, 'manifest.xml' ) # The manifest.xml file has already been validated, so no error_message should be returned here. - repository_info_dicts, error_message = import_util.get_repository_info_from_manifest( manifest_file_path ) + repository_info_dicts, error_message = irm.get_repository_info_from_manifest( manifest_file_path ) # Determine the status for each exported repository archive contained within the capsule. - repository_status_info_dicts = import_util.get_repository_status_from_tool_shed( trans.app, - trans.user, - trans.user_is_admin(), - repository_info_dicts ) + repository_status_info_dicts = irm.get_repository_status_from_tool_shed( repository_info_dicts ) # Generate a list of repository name / import results message tuples for display after the capsule is imported. import_results_tups = [] # Only create repositories that do not yet exist and that the current user is authorized to create. The @@ -280,12 +281,9 @@ # Add the capsule_file_name and encoded_file_path to the repository_status_info_dict. repository_status_info_dict[ 'capsule_file_name' ] = capsule_file_name repository_status_info_dict[ 'encoded_file_path' ] = encoded_file_path - import_results_tups = import_util.create_repository_and_import_archive( trans.app, - trans.request.host, - trans.user, - repository_status_info_dict, - import_results_tups ) - import_util.check_status_and_reset_downloadable( trans.app, import_results_tups ) + import_results_tups = irm.create_repository_and_import_archive( repository_status_info_dict, + import_results_tups ) + irm.check_status_and_reset_downloadable( import_results_tups ) basic_util.remove_dir( file_path ) # NOTE: the order of installation is defined in import_results_tups, but order will be lost # when transferred to return_dict. diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 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 @@ -5,7 +5,7 @@ from galaxy import util from galaxy.model.orm import and_, not_, select from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest -from tool_shed.util import export_util +from tool_shed.capsule import capsule_manager from tool_shed.util import hg_util import tool_shed.util.shed_util_common as suc @@ -53,15 +53,14 @@ log.debug( error_message ) return None, error_message repository_id = trans.security.encode_id( repository.id ) - return export_util.export_repository( trans.app, - trans.user, - tool_shed_url, - repository_id, - str( repository.name ), - changeset_revision, - file_type, - export_repository_dependencies, - api=True ) + erm = capsule_manager.ExportRepositoryManager( app=trans.app, + user=trans.user, + tool_shed_url=tool_shed_url, + repository=repository, + changeset_revision=changeset_revision, + export_repository_dependencies=export_repository_dependencies, + using_api=True ) + return erm.export_repository() def __get_value_mapper( self, trans ): value_mapper = { 'id' : trans.security.encode_id, diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -14,20 +14,19 @@ from galaxy.web.framework.helpers import grids from galaxy.util import json from galaxy.model.orm import and_ -import tool_shed.util.shed_util_common as suc +from tool_shed.capsule import capsule_manager from tool_shed.util import basic_util from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import encoding_util -from tool_shed.util import export_util from tool_shed.util import hg_util -from tool_shed.util import import_util from tool_shed.util import metadata_util from tool_shed.util import readme_util from tool_shed.util import repository_dependency_util from tool_shed.util import repository_maintenance_util from tool_shed.util import review_util from tool_shed.util import search_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import workflow_util @@ -1149,7 +1148,7 @@ # server account's .hgrc file to include the following setting: # [web] # allow_archive = bz2, gz, zip - file_type_str = export_util.get_file_type_str( changeset_revision, file_type ) + file_type_str = basic_util.get_file_type_str( changeset_revision, file_type ) repository.times_downloaded += 1 trans.sa_session.add( repository ) trans.sa_session.flush() @@ -1172,15 +1171,14 @@ file_type = 'gz' export_repository_dependencies = CheckboxField.is_checked( export_repository_dependencies ) tool_shed_url = web.url_for( '/', qualified=True ) - repositories_archive, error_message = export_util.export_repository( trans.app, - trans.user, - tool_shed_url, - repository_id, - str( repository.name ), - changeset_revision, - file_type, - export_repository_dependencies, - api=False ) + erm = capsule_manager.ExportRepositoryManager( app=trans.app, + user=trans.user, + tool_shed_url=tool_shed_url, + repository=repository, + changeset_revision=changeset_revision, + export_repository_dependencies=export_repository_dependencies, + using_api=False ) + repositories_archive, error_message = erm.export_repository() repositories_archive_filename = os.path.basename( repositories_archive.name ) if error_message: message = error_message @@ -1969,15 +1967,16 @@ encoded_file_path = kwd.get( 'encoded_file_path', None ) file_path = encoding_util.tool_shed_decode( encoded_file_path ) export_info_file_path = os.path.join( file_path, 'export_info.xml' ) - export_info_dict = import_util.get_export_info_dict( export_info_file_path ) + irm = capsule_manager.ImportRepositoryManager( trans.app, + trans.request.host, + trans.user, + trans.user_is_admin() ) + export_info_dict = irm.get_export_info_dict( export_info_file_path ) manifest_file_path = os.path.join( file_path, 'manifest.xml' ) # The manifest.xml file has already been validated, so no error_message should be returned here. - repository_info_dicts, error_message = import_util.get_repository_info_from_manifest( manifest_file_path ) + repository_info_dicts, error_message = irm.get_repository_info_from_manifest( manifest_file_path ) # Determine the status for each exported repository archive contained within the capsule. - repository_status_info_dicts = import_util.get_repository_status_from_tool_shed( trans.app, - trans.user, - trans.user_is_admin(), - repository_info_dicts ) + repository_status_info_dicts = irm.get_repository_status_from_tool_shed( repository_info_dicts ) if 'import_capsule_button' in kwd: # Generate a list of repository name / import results message tuples for display after the capsule is imported. import_results_tups = [] @@ -1987,12 +1986,9 @@ # Add the capsule_file_name and encoded_file_path to the repository_status_info_dict. repository_status_info_dict[ 'capsule_file_name' ] = capsule_file_name repository_status_info_dict[ 'encoded_file_path' ] = encoded_file_path - import_results_tups = import_util.create_repository_and_import_archive( trans.app, - trans.request.host, - trans.user, - repository_status_info_dict, - import_results_tups ) - import_util.check_status_and_reset_downloadable( trans.app, import_results_tups ) + import_results_tups = irm.create_repository_and_import_archive( repository_status_info_dict, + import_results_tups ) + irm.check_status_and_reset_downloadable( import_results_tups ) basic_util.remove_dir( file_path ) return trans.fill_template( '/webapps/tool_shed/repository/import_capsule_results.mako', export_info_dict=export_info_dict, @@ -3081,13 +3077,17 @@ status = kwd.get( 'status', 'done' ) url = kwd.get( 'url', '' ) if 'upload_capsule_button' in kwd: - capsule_dict = import_util.upload_capsule( **kwd ) + irm = capsule_manager.ImportRepositoryManager( trans.app, + trans.request.host, + trans.user, + trans.user_is_admin() ) + capsule_dict = irm.upload_capsule( **kwd ) status = capsule_dict.get( 'status', 'error' ) if status == 'error': message = capsule_dict.get( 'error_message', '' ) else: - capsule_dict = import_util.extract_capsule_files( **capsule_dict ) - capsule_dict = import_util.validate_capsule( **capsule_dict ) + capsule_dict = irm.extract_capsule_files( **capsule_dict ) + capsule_dict = irm.validate_capsule( **capsule_dict ) status = capsule_dict.get( 'status', 'error' ) if status == 'ok': return trans.response.send_redirect( web.url_for( controller='repository', diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/capsule/capsule_manager.py --- /dev/null +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -0,0 +1,867 @@ +import logging +import os +import shutil +import tarfile +import tempfile +import threading +import urllib +from time import gmtime +from time import strftime +import tool_shed.repository_types.util as rt_util +from galaxy import web +from galaxy.util import asbool +from galaxy.util import CHUNK_SIZE +from galaxy.util.odict import odict +from tool_shed.dependencies import dependency_manager +from tool_shed.util import basic_util +from tool_shed.util import commit_util +from tool_shed.util import common_util +from tool_shed.util import encoding_util +from tool_shed.util import hg_util +from tool_shed.util import metadata_util +from tool_shed.util import repository_dependency_util +from tool_shed.util import repository_maintenance_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util +from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager + +log = logging.getLogger( __name__ ) + + +class ExportedRepositoryRegistry( object ): + + def __init__( self ): + self.exported_repository_elems = [] + +class ExportRepositoryManager( object ): + + def __init__( self, app, user, tool_shed_url, repository, changeset_revision, export_repository_dependencies, using_api ): + self.app = app + self.capsule_filename = 'capsule' + self.capsule_with_dependencies_filename = 'capsule_with_dependencies' + self.changeset_revision = changeset_revision + self.export_repository_dependencies = asbool( export_repository_dependencies ) + self.file_type = 'gz' + self.repository = repository + self.repository_id = self.app.security.encode_id( repository.id ) + self.tool_shed_url = tool_shed_url + self.user = user + self.using_api = using_api + + def export_repository( self ): + repositories_archive_filename = self.generate_repository_archive_filename( use_tmp_archive_dir=True ) + if self.export_repository_dependencies: + repo_info_dicts = self.get_repo_info_dicts() + repository_ids = self.get_repository_ids( repo_info_dicts ) + ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = \ + self.order_components_for_import( repository_ids, repo_info_dicts ) + else: + ordered_repository_ids = [] + ordered_repositories = [] + ordered_changeset_revisions = [] + if self.repository: + repository_metadata = \ + suc.get_current_repository_metadata_for_changeset_revision( self.app, + self.repository, + self.changeset_revision ) + if repository_metadata: + ordered_repository_ids = [ self.repository_id ] + ordered_repositories = [ self.repository ] + ordered_changeset_revisions = [ repository_metadata.changeset_revision ] + repositories_archive = None + error_messages = '' + lock = threading.Lock() + lock.acquire( True ) + try: + repositories_archive = tarfile.open( repositories_archive_filename, "w:%s" % self.file_type ) + exported_repository_registry = ExportedRepositoryRegistry() + for index, repository_id in enumerate( ordered_repository_ids ): + work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-export-er" ) + ordered_repository = ordered_repositories[ index ] + ordered_changeset_revision = ordered_changeset_revisions[ index ] + repository_archive, error_message = self.generate_repository_archive( ordered_repository, + ordered_changeset_revision, + work_dir ) + if error_message: + error_messages = '%s %s' % ( error_messages, error_message ) + else: + archive_name = str( os.path.basename( repository_archive.name ) ) + repositories_archive.add( repository_archive.name, arcname=archive_name ) + attributes, sub_elements = self.get_repository_attributes_and_sub_elements( ordered_repository, + archive_name ) + elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) + exported_repository_registry.exported_repository_elems.append( elem ) + basic_util.remove_dir( work_dir ) + # Keep information about the export in a file named export_info.xml in the archive. + sub_elements = self.generate_export_elem() + export_elem = xml_util.create_element( 'export_info', attributes=None, sub_elements=sub_elements ) + tmp_export_info = xml_util.create_and_write_tmp_file( export_elem, use_indent=True ) + repositories_archive.add( tmp_export_info, arcname='export_info.xml' ) + # Write the manifest, which must preserve the order in which the repositories should be imported. + exported_repository_root = xml_util.create_element( 'repositories' ) + for exported_repository_elem in exported_repository_registry.exported_repository_elems: + exported_repository_root.append( exported_repository_elem ) + tmp_manifest = xml_util.create_and_write_tmp_file( exported_repository_root, use_indent=True ) + repositories_archive.add( tmp_manifest, arcname='manifest.xml' ) + except Exception, e: + log.exception( str( e ) ) + finally: + lock.release() + if repositories_archive is not None: + repositories_archive.close() + if self.using_api: + encoded_repositories_archive_name = encoding_util.tool_shed_encode( repositories_archive_filename ) + params = '?encoded_repositories_archive_name=%s' % encoded_repositories_archive_name + download_url = common_util.url_join( web.url_for( '/', qualified=True ), + 'repository/export_via_api%s' % params ) + return dict( download_url=download_url, error_messages=error_messages ) + return repositories_archive, error_messages + + def generate_export_elem( self ): + sub_elements = odict() + sub_elements[ 'export_time' ] = strftime( '%a, %d %b %Y %H:%M:%S +0000', gmtime() ) + sub_elements[ 'tool_shed' ] = str( self.tool_shed_url.rstrip( '/' ) ) + sub_elements[ 'repository_name' ] = str( self.repository.name ) + sub_elements[ 'repository_owner' ] = str( self.repository.user.username ) + sub_elements[ 'changeset_revision' ] = str( self.changeset_revision ) + sub_elements[ 'export_repository_dependencies' ] = str( self.export_repository_dependencies ) + sub_elements[ 'exported_via_api' ] = str( self.using_api ) + return sub_elements + + def generate_repository_archive( self, repository, changeset_revision, work_dir ): + rdah = dependency_manager.RepositoryDependencyAttributeHandler( self.app, unpopulate=True ) + tdah = dependency_manager.ToolDependencyAttributeHandler( self.app, unpopulate=True ) + file_type_str = basic_util.get_file_type_str( changeset_revision, self.file_type ) + file_name = '%s-%s' % ( repository.name, file_type_str ) + return_code, error_message = hg_util.archive_repository_revision( self.app, + repository, + work_dir, + changeset_revision ) + if return_code: + return None, error_message + repository_archive_name = os.path.join( work_dir, file_name ) + # Create a compressed tar archive that will contain only valid files and possibly altered dependency definition files. + repository_archive = tarfile.open( repository_archive_name, "w:%s" % self.file_type ) + for root, dirs, files in os.walk( work_dir ): + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + for dir in dirs: + if dir in commit_util.UNDESIRABLE_DIRS: + dirs.remove( dir ) + for name in files: + name = str( name ) + if str( name ) in commit_util.UNDESIRABLE_FILES: + continue + full_path = os.path.join( root, name ) + relative_path = full_path.replace( work_dir, '' ).lstrip( '/' ) + # See if we have a repository dependencies defined. + if name == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: + # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. + altered, root_elem, error_message = rdah.handle_tag_attributes( full_path ) + if error_message: + return None, error_message + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) + shutil.move( tmp_filename, full_path ) + elif name == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: + # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. + altered, root_elem, error_message = tdah.handle_tag_attributes( full_path ) + if error_message: + return None, error_message + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) + shutil.move( tmp_filename, full_path ) + repository_archive.add( full_path, arcname=relative_path ) + repository_archive.close() + return repository_archive, error_message + + def generate_repository_archive_filename( self, use_tmp_archive_dir=False ): + tool_shed = self.remove_protocol_from_tool_shed_url() + file_type_str = basic_util.get_file_type_str( self.changeset_revision, self.file_type ) + if self.export_repository_dependencies: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( self.capsule_with_dependencies_filename, + tool_shed, + str( self.repository.name ), + str( self.repository.user.username ), + file_type_str ) + else: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( self.capsule_filename, + tool_shed, + str( self.repository.name ), + str( self.repository.user.username ), + file_type_str ) + if use_tmp_archive_dir: + tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" ) + repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename ) + return repositories_archive_filename + + def get_components_from_repo_info_dict( self, repo_info_dict ): + """ + Return the repository and the associated latest installable changeset_revision (including + # updates) for the repository defined by the received repo_info_dict. + """ + for repository_name, repo_info_tup in repo_info_dict.items(): + # There should only be one entry in the received repo_info_dict. + description, \ + repository_clone_url, \ + changeset_revision, \ + ctx_rev, \ + repository_owner, \ + repository_dependencies, \ + tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tup ) + repository = suc.get_repository_by_name_and_owner( self.app, repository_name, repository_owner ) + repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( self.app, + repository, + changeset_revision ) + if repository_metadata: + return repository, repository_metadata.changeset_revision + return None, None + + def get_repo_info_dict_for_import( self, encoded_repository_id, encoded_repository_ids, repo_info_dicts ): + """ + The received encoded_repository_ids and repo_info_dicts are lists that contain associated + elements at each location in the list. This method will return the element from repo_info_dicts + associated with the received encoded_repository_id by determining its location in the received + encoded_repository_ids list. + """ + for index, repository_id in enumerate( encoded_repository_ids ): + if repository_id == encoded_repository_id: + repo_info_dict = repo_info_dicts[ index ] + return repo_info_dict + return None + + def get_repo_info_dicts( self ): + """ + Return a list of dictionaries defining repositories that are required by the repository + associated with self.repository_id. + """ + rdm = RepositoryDependencyManager( self.app ) + repository = suc.get_repository_in_tool_shed( self.app, self.repository_id ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + self.repository_id, + self.changeset_revision ) + # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. + toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) + repository_dependencies = \ + repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=self.app, + repository=self.repository, + repository_metadata=repository_metadata, + toolshed_base_url=toolshed_base_url, + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None ) + repo = hg_util.get_repo_for_repository( self.app, + repository=self.repository, + repo_path=None, + create=False ) + ctx = hg_util.get_changectx_for_changeset( repo, self.changeset_revision ) + repo_info_dict = {} + # Cast unicode to string. + repo_info_dict[ str( repository.name ) ] = ( str( self.repository.description ), + common_util.generate_clone_url_for_repository_in_tool_shed( self.user, + self.repository ), + str( self.changeset_revision ), + str( ctx.rev() ), + str( self.repository.user.username ), + repository_dependencies, + None ) + all_required_repo_info_dict = rdm.get_required_repo_info_dicts( self.tool_shed_url, [ repo_info_dict ] ) + all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] ) + return all_repo_info_dicts + + def get_repository_attributes_and_sub_elements( self, repository, archive_name ): + """ + Get the information about a repository to create and populate an XML tag set. The + generated attributes will be contained within the <repository> tag, while the sub_elements + will be tag sets contained within the <repository> tag set. + """ + attributes = odict() + sub_elements = odict() + attributes[ 'name' ] = str( repository.name ) + attributes[ 'type' ] = str( repository.type ) + # We have to associate the public username since the user_id will be different between tool sheds. + attributes[ 'username' ] = str( repository.user.username ) + # Don't coerce description or long description from unicode to string because the fields are free text. + sub_elements[ 'description' ] = repository.description + sub_elements[ 'long_description' ] = repository.long_description + sub_elements[ 'archive' ] = archive_name + # Keep track of Category associations. + categories = [] + for rca in repository.categories: + category = rca.category + categories.append( ( 'category', str( category.name ) ) ) + sub_elements[ 'categories' ] = categories + return attributes, sub_elements + + def get_repository_ids( self, repo_info_dicts ): + """Return a list of repository ids associated with each dictionary in the received repo_info_dicts.""" + repository_ids = [] + for repo_info_dict in repo_info_dicts: + for repository_name, repo_info_tup in repo_info_dict.items(): + description, \ + repository_clone_url, \ + changeset_revision, \ + ctx_rev, \ + repository_owner, \ + repository_dependencies, \ + tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tup ) + repository = suc.get_repository_by_name_and_owner( self.app, repository_name, repository_owner ) + repository_ids.append( self.app.security.encode_id( repository.id ) ) + return repository_ids + + def order_components_for_import( self, repository_ids, repo_info_dicts ): + """ + Some repositories may have repository dependencies that must be imported and have metadata set on + them before the dependent repository is imported. This method will inspect the list of repositories + about to be exported and make sure to order them appropriately for proper import. For each repository + about to be exported, if required repositories are not contained in the list of repositories about to + be exported, then they are not considered. Repository dependency definitions that contain circular + dependencies should not result in an infinite loop, but obviously ordering the list will not be handled + for one or more of the repositories that require prior import. + """ + # The received list of repository_ids are the ids of all of the primary exported repository's + # repository dependencies. The primary repository will always be last in the returned lists. + ordered_repository_ids = [] + ordered_repositories = [] + ordered_changeset_revisions = [] + # Create a dictionary whose keys are the received repository_ids and whose values are a list of + # repository_ids, each of which is contained in the received list of repository_ids and whose associated + # repository must be imported prior to the repository associated with the repository_id key. + prior_import_required_dict = suc.get_prior_import_or_install_required_dict( self.app, + repository_ids, + repo_info_dicts ) + processed_repository_ids = [] + # Process the list of repository dependencies defined for the primary exported repository. + while len( processed_repository_ids ) != len( prior_import_required_dict.keys() ): + repository_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_import_required_dict, + processed_repository_ids ) + if repository_id == self.repository_id: + # Append self.repository_id without processing it since it must be returned last in the order. + # It will be processed below after all dependencies are processed. + processed_repository_ids.append( self.repository_id ) + continue + processed_repository_ids.append( repository_id ) + if repository_id not in ordered_repository_ids: + prior_import_required_ids = prior_import_required_dict[ repository_id ] + for prior_import_required_id in prior_import_required_ids: + if prior_import_required_id not in ordered_repository_ids: + # Import the associated repository dependency first. + prior_repo_info_dict = \ + self.get_repo_info_dict_for_import( prior_import_required_id, + repository_ids, + repo_info_dicts ) + prior_repository, prior_import_changeset_revision = \ + self.get_components_from_repo_info_dict( prior_repo_info_dict ) + if prior_repository and prior_import_changeset_revision: + ordered_repository_ids.append( prior_import_required_id ) + ordered_repositories.append( prior_repository ) + ordered_changeset_revisions.append( prior_import_changeset_revision ) + repo_info_dict = self.get_repo_info_dict_for_import( repository_id, repository_ids, repo_info_dicts ) + repository, changeset_revision = self.get_components_from_repo_info_dict( repo_info_dict ) + if repository and changeset_revision: + ordered_repository_ids.append( repository_id ) + ordered_repositories.append( repository ) + ordered_changeset_revisions.append( changeset_revision ) + # Process the repository associated with self.repository_id last. + repo_info_dict = self.get_repo_info_dict_for_import( self.repository_id, repository_ids, repo_info_dicts ) + repository, changeset_revision = self.get_components_from_repo_info_dict( repo_info_dict ) + if repository and changeset_revision: + ordered_repository_ids.append( repository_id ) + ordered_repositories.append( repository ) + ordered_changeset_revisions.append( changeset_revision ) + return ordered_repository_ids, ordered_repositories, ordered_changeset_revisions + + def remove_protocol_from_tool_shed_url( self ): + protocol, base = self.tool_shed_url.split( '://' ) + base = base.replace( ':', '_colon_' ) + base = base.rstrip( '/' ) + return base + + +class ImportRepositoryManager( object ): + + def __init__( self, app, host, user, user_is_admin ): + self.app = app + self.host = host + self.user = user + self.user_is_admin = user_is_admin + + def check_status_and_reset_downloadable( self, import_results_tups ): + """Check the status of each imported repository and set downloadable to False if errors.""" + sa_session = self.app.model.context.current + flush = False + for import_results_tup in import_results_tups: + ok, name_owner, message = import_results_tup + name, owner = name_owner + if not ok: + repository = suc.get_repository_by_name_and_owner( self.app, name, owner ) + if repository is not None: + # Do not allow the repository to be automatically installed if population resulted in errors. + tip_changeset_revision = repository.tip( self.app ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + self.app.security.encode_id( repository.id ), + tip_changeset_revision ) + if repository_metadata: + if repository_metadata.downloadable: + repository_metadata.downloadable = False + sa_session.add( repository_metadata ) + if not flush: + flush = True + # Do not allow dependent repository revisions to be automatically installed if population + # resulted in errors. + dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( self.app, repository_metadata ) + for dependent_downloadable_revision in dependent_downloadable_revisions: + if dependent_downloadable_revision.downloadable: + dependent_downloadable_revision.downloadable = False + sa_session.add( dependent_downloadable_revision ) + if not flush: + flush = True + if flush: + sa_session.flush() + + def create_repository_and_import_archive( self, repository_archive_dict, import_results_tups ): + """ + Create a new repository in the tool shed and populate it with the contents of a gzip compressed + tar archive that was exported as part or all of the contents of a capsule. + """ + results_message = '' + name = repository_archive_dict.get( 'name', None ) + username = repository_archive_dict.get( 'owner', None ) + if name is None or username is None: + ok = False + results_message += 'Import failed: required repository name <b>%s</b> or owner <b>%s</b> is missing.' % \ + ( str( name ), str( username )) + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + else: + status = repository_archive_dict.get( 'status', None ) + if status is None: + # The repository does not yet exist in this Tool Shed and the current user is authorized to import + # the current archive file. + type = repository_archive_dict.get( 'type', 'unrestricted' ) + description = repository_archive_dict.get( 'description', '' ) + long_description = repository_archive_dict.get( 'long_description', '' ) + # The owner entry in the repository_archive_dict is the public username of the user associated with + # the exported repository archive. + user = suc.get_user_by_username( self.app, username ) + if user is None: + ok = False + results_message += 'Import failed: repository owner <b>%s</b> does not have an account in this Tool Shed.' % \ + str( username ) + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + else: + user_id = user.id + # The categories entry in the repository_archive_dict is a list of category names. If a name does not + # exist in the current Tool Shed, the category will not be created, so it will not be associated with + # the repository. + category_ids = [] + category_names = repository_archive_dict.get( 'category_names', [] ) + for category_name in category_names: + category = suc.get_category_by_name( self.app, category_name ) + if category is None: + results_message += 'This Tool Shed does not have the category <b>%s</b> so it ' % str( category_name ) + results_message += 'will not be associated with this repository.' + else: + category_ids.append( self.app.security.encode_id( category.id ) ) + # Create the repository record in the database. + repository, create_message = repository_maintenance_util.create_repository( self.app, + name, + type, + description, + long_description, + user_id=user_id, + category_ids=category_ids ) + if create_message: + results_message += create_message + # Populate the new repository with the contents of exported repository archive. + results_dict = self.import_repository_archive( repository, repository_archive_dict ) + ok = results_dict.get( 'ok', False ) + error_message = results_dict.get( 'error_message', '' ) + if error_message: + results_message += error_message + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + else: + # The repository either already exists in this Tool Shed or the current user is not authorized to create it. + ok = True + results_message += 'Import not necessary: repository status for this Tool Shed is: %s.' % str( status ) + import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) + return import_results_tups + + def extract_capsule_files( self, **kwd ): + """ + Extract the uploaded capsule archive into a temporary location for inspection, validation + and potential import. + """ + return_dict = {} + tar_archive = kwd.get( 'tar_archive', None ) + capsule_file_name = kwd.get( 'capsule_file_name', None ) + if tar_archive is not None and capsule_file_name is not None: + return_dict.update( kwd ) + extract_directory_path = tempfile.mkdtemp( prefix="tmp-capsule-ecf" ) + if capsule_file_name.endswith( '.tar.gz' ): + extract_directory_name = capsule_file_name.replace( '.tar.gz', '' ) + elif capsule_file_name.endswith( '.tar' ): + extract_directory_name = capsule_file_name.replace( '.tar', '' ) + else: + extract_directory_name = capsule_file_name + file_path = os.path.join( extract_directory_path, extract_directory_name ) + return_dict[ 'encoded_file_path' ] = encoding_util.tool_shed_encode( file_path ) + tar_archive.extractall( path=file_path ) + try: + tar_archive.close() + except Exception, e: + log.exception( "Cannot close tar_archive: %s" % str( e ) ) + del return_dict[ 'tar_archive' ] + return return_dict + + def get_archives_from_manifest( self, manifest_file_path ): + """ + Return the list of archive names defined in the capsule manifest. This method will validate + the manifest by ensuring all <repository> tag sets contain a valid <archive> sub-element. + """ + archives = [] + error_message = '' + manifest_tree, error_message = xml_util.parse_xml( manifest_file_path ) + if error_message: + return archives, error_message + manifest_root = manifest_tree.getroot() + for elem in manifest_root: + # <repository name="package_lapack_3_4" type="tool_dependency_definition" username="test"> + if elem.tag != 'repository': + error_message = 'All level one sub-elements in the manifest.xml file must be <repository> tag sets. ' + error_message += 'The tag <b><%s></b> is invalid.' % str( elem.tag ) + return [], error_message + archive_file_name = None + for repository_elem in elem: + if repository_elem.tag == 'archive': + # <archive>package_lapack_3_4-9e7a45ad3522.tar.gz</archive> + archive_file_name = repository_elem.text + break + if archive_file_name is None: + error_message = 'The %s tag set is missing a required <archive> sub-element.' % str( elem.tag ) + return [], error_message + archives.append( archive_file_name ) + return archives, error_message + + def get_export_info_dict( self, export_info_file_path ): + """ + Parse the export_info.xml file contained within the capsule and return a dictionary + containing its entries. + """ + export_info_tree, error_message = xml_util.parse_xml( export_info_file_path ) + export_info_root = export_info_tree.getroot() + export_info_dict = {} + for elem in export_info_root: + if elem.tag == 'export_time': + export_info_dict[ 'export_time' ] = elem.text + elif elem.tag == 'tool_shed': + export_info_dict[ 'tool_shed' ] = elem.text + elif elem.tag == 'repository_name': + export_info_dict[ 'repository_name' ] = elem.text + elif elem.tag == 'repository_owner': + export_info_dict[ 'repository_owner' ] = elem.text + elif elem.tag == 'changeset_revision': + export_info_dict[ 'changeset_revision' ] = elem.text + elif elem.tag == 'export_repository_dependencies': + if asbool( elem.text ): + export_info_dict[ 'export_repository_dependencies' ] = 'Yes' + else: + export_info_dict[ 'export_repository_dependencies' ] = 'No' + return export_info_dict + + def get_repository_info_from_manifest( self, manifest_file_path ): + """ + Parse the capsule manifest and return a list of dictionaries containing information about + each exported repository archive contained within the capsule. + """ + repository_info_dicts = [] + manifest_tree, error_message = xml_util.parse_xml( manifest_file_path ) + if error_message: + return repository_info_dicts, error_message + manifest_root = manifest_tree.getroot() + for elem in manifest_root: + # <repository name="package_lapack_3_4" type="tool_dependency_definition" username="test"> + if elem.tag != 'repository': + error_message = 'All level one sub-elements in the manifest.xml file must be <repository> tag sets. ' + error_message += 'The tag <b><%s></b> is invalid.' % str( elem.tag ) + return [], error_message + name = elem.get( 'name', None ) + owner = elem.get( 'username', None ) + type = elem.get( 'type', None ) + if name is None or owner is None or type is None: + error_message = 'Missing required name, type, owner attributes from the tag %s' % str( elem.tag ) + return [], error_message + repository_info_dict = dict( name=name, owner=owner, type=type ) + for repository_elem in elem: + if repository_elem.tag == 'archive': + # <archive>package_lapack_3_4-9e7a45ad3522.tar.gz</archive> + archive_file_name = repository_elem.text + repository_info_dict[ 'archive_file_name' ] = archive_file_name + items = archive_file_name.split( '-' ) + changeset_revision = items[ 1 ].rstrip( '.tar.gz' ) + repository_info_dict [ 'changeset_revision' ] = changeset_revision + elif repository_elem.tag == 'categories': + category_names = [] + for category_elem in repository_elem: + if category_elem.tag == 'category': + category_names.append( category_elem.text ) + repository_info_dict[ 'category_names' ] = category_names + elif repository_elem.tag == 'description': + repository_info_dict[ 'description' ] = repository_elem.text + elif repository_elem.tag == 'long_description': + repository_info_dict[ 'long_description' ] = repository_elem.text + repository_info_dicts.append( repository_info_dict ) + return repository_info_dicts, error_message + + def get_repository_status_from_tool_shed( self, repository_info_dicts ): + """ + For each exported repository archive contained in the capsule, inspect the Tool Shed to + see if that repository already exists or if the current user is authorized to create the + repository and set a status appropriately. If repository dependencies are included in the + capsule, repositories may have various owners. We will keep repositories associated with + owners, so we need to restrict created repositories to those the current user can create. + If the current user is an admin or a member of the IUC, all repositories will be created + no matter the owner. Otherwise only repositories whose associated owner is the current + user will be created. + """ + repository_status_info_dicts = [] + for repository_info_dict in repository_info_dicts: + repository = suc.get_repository_by_name_and_owner( self.app, + repository_info_dict[ 'name' ], + repository_info_dict[ 'owner' ] ) + if repository: + if repository.deleted: + repository_info_dict[ 'status' ] = 'Exists, deleted' + elif repository.deprecated: + repository_info_dict[ 'status' ] = 'Exists, deprecated' + else: + repository_info_dict[ 'status' ] = 'Exists' + else: + # No repository with the specified name and owner currently exists, so make sure + # the current user can create one. + if self.user_is_admin: + repository_info_dict[ 'status' ] = None + elif self.app.security_agent.user_can_import_repository_archive( self.user, + repository_info_dict[ 'owner' ] ): + repository_info_dict[ 'status' ] = None + else: + repository_info_dict[ 'status' ] = 'Not authorized to import' + repository_status_info_dicts.append( repository_info_dict ) + return repository_status_info_dicts + + def import_repository_archive( self, repository, repository_archive_dict ): + """Import a repository archive contained within a repository capsule.""" + rdah = dependency_manager.RepositoryDependencyAttributeHandler( self.app, unpopulate=False ) + tdah = dependency_manager.ToolDependencyAttributeHandler( self.app, unpopulate=False ) + archive_file_name = repository_archive_dict.get( 'archive_file_name', None ) + capsule_file_name = repository_archive_dict[ 'capsule_file_name' ] + encoded_file_path = repository_archive_dict[ 'encoded_file_path' ] + file_path = encoding_util.tool_shed_decode( encoded_file_path ) + results_dict = dict( ok=True, error_message='' ) + archive_file_path = os.path.join( file_path, archive_file_name ) + archive = tarfile.open( archive_file_path, 'r:*' ) + repo_dir = repository.repo_path( self.app ) + repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) + undesirable_dirs_removed = 0 + undesirable_files_removed = 0 + ok, error_message = commit_util.check_archive( repository, archive ) + if ok: + full_path = os.path.abspath( repo_dir ) + filenames_in_archive = [] + for tarinfo_obj in archive.getmembers(): + # Check files and directories in the archive. + ok = os.path.basename( tarinfo_obj.name ) not in commit_util.UNDESIRABLE_FILES + if ok: + for file_path_item in tarinfo_obj.name.split( '/' ): + if file_path_item in commit_util.UNDESIRABLE_DIRS: + undesirable_dirs_removed += 1 + error_message = 'Import failed: invalid file path <b>%s</b> in archive <b>%s</b>' % \ + ( str( file_path_item ), str( archive_file_name ) ) + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + return results_dict + filenames_in_archive.append( tarinfo_obj.name ) + else: + undesirable_files_removed += 1 + # Extract the uploaded archive to the repository root. + archive.extractall( path=full_path ) + archive.close() + for filename in filenames_in_archive: + uploaded_file_name = os.path.join( full_path, filename ) + if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision attributes + # are missing and if so, set them appropriately. + altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if toolshed or changeset_revision + # attributes are missing and if so, set them appropriately. + altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + commit_message = 'Imported from capsule %s' % str( capsule_file_name ) + # Send email notification to those that have registered to receive alerts for new repositories in this Tool Shed. + new_repo_alert = True + # Since the repository is new, the following must be False. + remove_repo_files_not_in_tar = False + ok, error_message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ + commit_util.handle_directory_changes( self.app, + self.host, + self.user.username, + repository, + full_path, + filenames_in_archive, + remove_repo_files_not_in_tar, + new_repo_alert, + commit_message, + undesirable_dirs_removed, + undesirable_files_removed ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + try: + status, error_message = metadata_util.set_repository_metadata_due_to_new_tip( self.app, + self.host, + self.user, + repository, + content_alert_str=content_alert_str ) + if error_message: + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + except Exception, e: + log.debug( "Error setting metadata on repository %s created from imported archive %s: %s" % \ + ( str( repository.name ), str( archive_file_name ), str( e ) ) ) + else: + archive.close() + results_dict[ 'ok' ] = False + results_dict[ 'error_message' ] += error_message + return results_dict + + def upload_capsule( self, **kwd ): + """Upload and prepare an exported repository capsule for validation.""" + file_data = kwd.get( 'file_data', '' ) + url = kwd.get( 'url', '' ) + uploaded_file = None + return_dict = dict( error_message='', + encoded_file_path=None, + status='ok', + tar_archive=None, + uploaded_file=None, + capsule_file_name=None ) + if file_data == '' and url == '': + message = 'No files were entered on the import form.' + status = 'error' + elif url: + valid_url = True + try: + stream = urllib.urlopen( url ) + except Exception, e: + valid_url = False + message = 'Error importing file via http: %s' % str( e ) + status = 'error' + if valid_url: + fd, uploaded_file_name = tempfile.mkstemp() + uploaded_file = open( uploaded_file_name, 'wb' ) + while 1: + chunk = stream.read( CHUNK_SIZE ) + if not chunk: + break + uploaded_file.write( chunk ) + uploaded_file.flush() + uploaded_file_filename = url.split( '/' )[ -1 ] + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 + elif file_data not in ( '', None ): + uploaded_file = file_data.file + uploaded_file_name = uploaded_file.name + uploaded_file_filename = os.path.split( file_data.filename )[ -1 ] + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 + if uploaded_file is not None: + if isempty: + uploaded_file.close() + return_dict[ 'error_message' ] = 'Your uploaded capsule file is empty.' + return_dict[ 'status' ] = 'error' + return return_dict + try: + # Open for reading with transparent compression. + tar_archive = tarfile.open( uploaded_file_name, 'r:*' ) + except tarfile.ReadError, e: + error_message = 'Error opening file %s: %s' % ( str( uploaded_file_name ), str( e ) ) + log.exception( error_message ) + return_dict[ 'error_message' ] = error_message + return_dict[ 'status' ] = 'error' + uploaded_file.close() + return return_dict + return_dict[ 'tar_archive' ] = tar_archive + return_dict[ 'capsule_file_name' ] = uploaded_file_filename + uploaded_file.close() + else: + return_dict[ 'error_message' ] = 'No files were entered on the import form.' + return_dict[ 'status' ] = 'error' + return return_dict + return return_dict + + def validate_capsule( self, **kwd ): + """ + Inspect the uploaded capsule's manifest and its contained files to ensure it is a valid + repository capsule. + """ + capsule_dict = {} + capsule_dict.update( kwd ) + encoded_file_path = capsule_dict.get( 'encoded_file_path', '' ) + file_path = encoding_util.tool_shed_decode( encoded_file_path ) + # The capsule must contain a valid XML file named export_info.xml. + export_info_file_path = os.path.join( file_path, 'export_info.xml' ) + export_info_tree, error_message = xml_util.parse_xml( export_info_file_path ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + # The capsule must contain a valid XML file named manifest.xml. + manifest_file_path = os.path.join( file_path, 'manifest.xml' ) + # Validate the capsule manifest by inspecting name, owner, changeset_revision and type + # information contained within each <repository> tag set. + repository_info_dicts, error_message = self.get_repository_info_from_manifest( manifest_file_path ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + # Validate the capsule manifest by ensuring all <repository> tag sets contain a valid + # <archive> sub-element. + archives, error_message = self.get_archives_from_manifest( manifest_file_path ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + # Validate the capsule manifest by ensuring each defined archive file name exists within + # the capsule. + error_message = self.verify_archives_in_capsule( file_path, archives ) + if error_message: + capsule_dict[ 'error_message' ] = error_message + capsule_dict[ 'status' ] = 'error' + return capsule_dict + capsule_dict[ 'status' ] = 'ok' + return capsule_dict + + def verify_archives_in_capsule( self, file_path, archives ): + """ + Inspect the files contained within the capsule and make sure each is defined correctly + in the capsule manifest. + """ + error_message = '' + for archive_file_name in archives: + full_path = os.path.join( file_path, archive_file_name ) + if not os.path.exists( full_path ): + error_message = 'The uploaded capsule is invalid because the contained manifest.xml ' + error_message += 'file defines an archive file named <b>%s</b> which ' % str( archive_file_name ) + error_message += 'is not contained within the capsule.' + break + return error_message diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/scripts/api/export.py --- a/lib/tool_shed/scripts/api/export.py +++ b/lib/tool_shed/scripts/api/export.py @@ -1,6 +1,7 @@ #!/usr/bin/env python """ -Export a specified repository revision and optionally all of its defined repository dependencies from the tool shed into a compressed archive. +Export a specified repository revision and optionally all of its defined repository +dependencies from the tool shed into a compressed archive. Here is a working example of how to use this script to export a repository from the tool shed. ./export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp @@ -8,15 +9,45 @@ import os import sys +import tempfile import argparse import urllib2 sys.path.insert( 0, os.path.dirname( __file__ ) ) from common import display from common import submit -from tool_shed.util import export_util +from tool_shed.util import basic_util +CAPSULE_FILENAME = 'capsule' +CAPSULE_WITH_DEPENDENCIES_FILENAME = 'capsule_with_dependencies' CHUNK_SIZE = 2**20 # 1Mb +def generate_repository_archive_filename( tool_shed_url, name, owner, changeset_revision, file_type, + export_repository_dependencies, use_tmp_archive_dir=False ): + tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url ) + file_type_str = basic_util.get_file_type_str( changeset_revision, file_type ) + if self.export_repository_dependencies: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_WITH_DEPENDENCIES_FILENAME, + tool_shed, + name, + owner, + file_type_str ) + else: + repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_FILENAME, + tool_shed, + name, + owner, + file_type_str ) + if use_tmp_archive_dir: + tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" ) + repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename ) + return repositories_archive_filename + +def remove_protocol_from_tool_shed_url( tool_shed_url ): + protocol, base = tool_shed_url.split( '://' ) + base = base.replace( ':', '_colon_' ) + base = base.rstrip( '/' ) + return base + def string_as_bool( string ): if str( string ).lower() in ( 'true', 'yes', 'on' ): return True @@ -50,14 +81,15 @@ if error_messages: print "Error attempting to export revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner, ":\n", error_messages else: + export_repository_dependencies = string_as_bool( options.export_repository_dependencies ) repositories_archive_filename = \ - export_util.generate_repository_archive_filename( base_tool_shed_url, - options.name, - options.owner, - options.changeset_revision, - file_type, - export_repository_dependencies=string_as_bool( options.export_repository_dependencies ), - use_tmp_archive_dir=False ) + generate_repository_archive_filename( base_tool_shed_url, + options.name, + options.owner, + options.changeset_revision, + file_type, + export_repository_dependencies=export_repository_dependencies, + use_tmp_archive_dir=False ) download_url = export_dict[ 'download_url' ] download_dir = os.path.abspath( options.download_dir ) file_path = os.path.join( download_dir, repositories_archive_filename ) diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -45,6 +45,17 @@ env_var_dict[ '__is64bit__' ] = sys.maxsize > 2**32 return env_var_dict +def get_file_type_str( changeset_revision, file_type ): + if file_type == 'zip': + file_type_str = '%s.zip' % changeset_revision + elif file_type == 'bz2': + file_type_str = '%s.tar.bz2' % changeset_revision + elif file_type == 'gz': + file_type_str = '%s.tar.gz' % changeset_revision + else: + file_type_str = '' + return file_type_str + def move_file( current_dir, source, destination, rename_to=None ): source_path = os.path.abspath( os.path.join( current_dir, source ) ) source_file = os.path.basename( source_path ) diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/util/export_util.py --- a/lib/tool_shed/util/export_util.py +++ /dev/null @@ -1,355 +0,0 @@ -import logging -import os -import shutil -import tarfile -import tempfile -import threading -from time import gmtime -from time import strftime -import tool_shed.repository_types.util as rt_util -from galaxy import web -from galaxy.util.odict import odict -from tool_shed.dependencies import dependency_manager -from tool_shed.util import basic_util -from tool_shed.util import commit_util -from tool_shed.util import common_util -from tool_shed.util import encoding_util -from tool_shed.util import hg_util -from tool_shed.util import repository_dependency_util -from tool_shed.util import shed_util_common as suc -from tool_shed.util import xml_util -from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager - -log = logging.getLogger( __name__ ) - -CAPSULE_FILENAME = 'capsule' -CAPSULE_WITH_DEPENDENCIES_FILENAME = 'capsule_with_dependencies' - -class ExportedRepositoryRegistry( object ): - - def __init__( self ): - self.exported_repository_elems = [] - -def export_repository( app, user, tool_shed_url, repository_id, repository_name, changeset_revision, file_type, - export_repository_dependencies, api=False ): - repository = suc.get_repository_in_tool_shed( app, repository_id ) - repositories_archive_filename = generate_repository_archive_filename( tool_shed_url, - str( repository.name ), - str( repository.user.username ), - changeset_revision, - file_type, - export_repository_dependencies=export_repository_dependencies, - use_tmp_archive_dir=True ) - if export_repository_dependencies: - repo_info_dicts = get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision ) - repository_ids = get_repository_ids( app, repo_info_dicts ) - ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = \ - order_components_for_import( app, repository_id, repository_ids, repo_info_dicts ) - else: - ordered_repository_ids = [] - ordered_repositories = [] - ordered_changeset_revisions = [] - if repository: - repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app, - repository, - changeset_revision ) - if repository_metadata: - ordered_repository_ids = [ repository_id ] - ordered_repositories = [ repository ] - ordered_changeset_revisions = [ repository_metadata.changeset_revision ] - repositories_archive = None - error_messages = '' - lock = threading.Lock() - lock.acquire( True ) - try: - repositories_archive = tarfile.open( repositories_archive_filename, "w:%s" % file_type ) - exported_repository_registry = ExportedRepositoryRegistry() - for index, repository_id in enumerate( ordered_repository_ids ): - work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-export-er" ) - ordered_repository = ordered_repositories[ index ] - ordered_changeset_revision = ordered_changeset_revisions[ index ] - repository_archive, error_message = generate_repository_archive( app, - work_dir, - tool_shed_url, - ordered_repository, - ordered_changeset_revision, - file_type ) - if error_message: - error_messages = '%s %s' % ( error_messages, error_message ) - else: - archive_name = str( os.path.basename( repository_archive.name ) ) - repositories_archive.add( repository_archive.name, arcname=archive_name ) - attributes, sub_elements = get_repository_attributes_and_sub_elements( ordered_repository, archive_name ) - elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) - exported_repository_registry.exported_repository_elems.append( elem ) - basic_util.remove_dir( work_dir ) - # Keep information about the export in a file name export_info.xml in the archive. - sub_elements = generate_export_elem( tool_shed_url, repository, changeset_revision, export_repository_dependencies, api ) - export_elem = xml_util.create_element( 'export_info', attributes=None, sub_elements=sub_elements ) - tmp_export_info = xml_util.create_and_write_tmp_file( export_elem, use_indent=True ) - repositories_archive.add( tmp_export_info, arcname='export_info.xml' ) - # Write the manifest, which must preserve the order in which the repositories should be imported. - exported_repository_root = xml_util.create_element( 'repositories' ) - for exported_repository_elem in exported_repository_registry.exported_repository_elems: - exported_repository_root.append( exported_repository_elem ) - tmp_manifest = xml_util.create_and_write_tmp_file( exported_repository_root, use_indent=True ) - repositories_archive.add( tmp_manifest, arcname='manifest.xml' ) - except Exception, e: - log.exception( str( e ) ) - finally: - lock.release() - repositories_archive.close() - if api: - encoded_repositories_archive_name = encoding_util.tool_shed_encode( repositories_archive_filename ) - params = '?encoded_repositories_archive_name=%s' % encoded_repositories_archive_name - download_url = common_util.url_join( web.url_for( '/', qualified=True ), - 'repository/export_via_api%s' % params ) - return dict( download_url=download_url, error_messages=error_messages ) - return repositories_archive, error_messages - -def generate_repository_archive( app, work_dir, tool_shed_url, repository, changeset_revision, file_type ): - rdah = dependency_manager.RepositoryDependencyAttributeHandler( app, unpopulate=True ) - tdah = dependency_manager.ToolDependencyAttributeHandler( app, unpopulate=True ) - file_type_str = get_file_type_str( changeset_revision, file_type ) - file_name = '%s-%s' % ( repository.name, file_type_str ) - return_code, error_message = hg_util.archive_repository_revision( app, - repository, - work_dir, - changeset_revision ) - if return_code: - return None, error_message - repository_archive_name = os.path.join( work_dir, file_name ) - # Create a compressed tar archive that will contain only valid files and possibly altered dependency definition files. - repository_archive = tarfile.open( repository_archive_name, "w:%s" % file_type ) - for root, dirs, files in os.walk( work_dir ): - if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: - for dir in dirs: - if dir in commit_util.UNDESIRABLE_DIRS: - dirs.remove( dir ) - for name in files: - name = str( name ) - if str( name ) in commit_util.UNDESIRABLE_FILES: - continue - full_path = os.path.join( root, name ) - relative_path = full_path.replace( work_dir, '' ).lstrip( '/' ) - # See if we have a repository dependencies defined. - if name == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: - # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. - altered, root_elem, error_message = rdah.handle_tag_attributes( full_path ) - if error_message: - return None, error_message - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) - shutil.move( tmp_filename, full_path ) - elif name == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME: - # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. - altered, root_elem, error_message = tdah.handle_tag_attributes( full_path ) - if error_message: - return None, error_message - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True ) - shutil.move( tmp_filename, full_path ) - repository_archive.add( full_path, arcname=relative_path ) - repository_archive.close() - return repository_archive, error_message - -def generate_repository_archive_filename( tool_shed_url, name, owner, changeset_revision, file_type, - export_repository_dependencies=False, use_tmp_archive_dir=False ): - tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url ) - file_type_str = get_file_type_str( changeset_revision, file_type ) - if export_repository_dependencies: - repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_WITH_DEPENDENCIES_FILENAME, tool_shed, name, owner, file_type_str ) - else: - repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_FILENAME, tool_shed, name, owner, file_type_str ) - if use_tmp_archive_dir: - tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" ) - repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename ) - return repositories_archive_filename - -def generate_export_elem( tool_shed_url, repository, changeset_revision, export_repository_dependencies, api ): - sub_elements = odict() - sub_elements[ 'export_time' ] = strftime( '%a, %d %b %Y %H:%M:%S +0000', gmtime() ) - sub_elements[ 'tool_shed' ] = str( tool_shed_url.rstrip( '/' ) ) - sub_elements[ 'repository_name' ] = str( repository.name ) - sub_elements[ 'repository_owner' ] = str( repository.user.username ) - sub_elements[ 'changeset_revision' ] = str( changeset_revision ) - sub_elements[ 'export_repository_dependencies' ] = str( export_repository_dependencies ) - sub_elements[ 'exported_via_api' ] = str( api ) - return sub_elements - -def get_components_from_repo_info_dict( app, repo_info_dict ): - """ - Return the repository and the associated latest installable changeset_revision (including updates) for the - repository defined by the received repo_info_dict. - """ - for repository_name, repo_info_tup in repo_info_dict.items(): - # There should only be one entry in the received repo_info_dict. - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tup ) - repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) - repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app, - repository, - changeset_revision ) - if repository_metadata: - return repository, repository_metadata.changeset_revision - return None, None - -def get_file_type_str( changeset_revision, file_type ): - if file_type == 'zip': - file_type_str = '%s.zip' % changeset_revision - elif file_type == 'bz2': - file_type_str = '%s.tar.bz2' % changeset_revision - elif file_type == 'gz': - file_type_str = '%s.tar.gz' % changeset_revision - else: - file_type_str = '' - return file_type_str - -def get_repo_info_dict_for_import( encoded_repository_id, encoded_repository_ids, repo_info_dicts ): - """ - The received encoded_repository_ids and repo_info_dicts are lists that contain associated elements at each - location in the list. This method will return the element from repo_info_dicts associated with the received - encoded_repository_id by determining its location in the received encoded_repository_ids list. - """ - for index, repository_id in enumerate( encoded_repository_ids ): - if repository_id == encoded_repository_id: - repo_info_dict = repo_info_dicts[ index ] - return repo_info_dict - return None - -def get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision ): - """ - Return a list of dictionaries defining repositories that are required by the repository associated with the - received repository_id. - """ - rdm = RepositoryDependencyManager( app ) - repository = suc.get_repository_in_tool_shed( app, repository_id ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, repository_id, changeset_revision ) - # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) - repository_dependencies = \ - repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=app, - repository=repository, - repository_metadata=repository_metadata, - toolshed_base_url=toolshed_base_url, - key_rd_dicts_to_be_processed=None, - all_repository_dependencies=None, - handled_key_rd_dicts=None ) - repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) - ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = {} - # Cast unicode to string. - repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), - common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ), - str( changeset_revision ), - str( ctx.rev() ), - str( repository.user.username ), - repository_dependencies, - None ) - all_required_repo_info_dict = rdm.get_required_repo_info_dicts( tool_shed_url, [ repo_info_dict ] ) - all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] ) - return all_repo_info_dicts - -def get_repository_attributes_and_sub_elements( repository, archive_name ): - """ - Get the information about a repository to create and populate an XML tag set. The generated attributes will - be contained within the <repository> tag, while the sub_elements will be tag sets contained within the <repository> - tag set. - """ - attributes = odict() - sub_elements = odict() - attributes[ 'name' ] = str( repository.name ) - attributes[ 'type' ] = str( repository.type ) - # We have to associate the public username since the user_id will be different between tool sheds. - attributes[ 'username' ] = str( repository.user.username ) - # Don't coerce description or long description from unicode to string because the fields are free text. - sub_elements[ 'description' ] = repository.description - sub_elements[ 'long_description' ] = repository.long_description - sub_elements[ 'archive' ] = archive_name - # Keep track of Category associations. - categories = [] - for rca in repository.categories: - category = rca.category - categories.append( ( 'category', str( category.name ) ) ) - sub_elements[ 'categories' ] = categories - return attributes, sub_elements - -def get_repository_ids( app, repo_info_dicts ): - """Return a list of repository ids associated with each dictionary in the received repo_info_dicts.""" - repository_ids = [] - for repo_info_dict in repo_info_dicts: - for repository_name, repo_info_tup in repo_info_dict.items(): - description, \ - repository_clone_url, \ - changeset_revision, \ - ctx_rev, \ - repository_owner, \ - repository_dependencies, \ - tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tup ) - repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) - repository_ids.append( app.security.encode_id( repository.id ) ) - return repository_ids - -def order_components_for_import( app, primary_repository_id, repository_ids, repo_info_dicts ): - """ - Some repositories may have repository dependencies that must be imported and have metadata set on - them before the dependent repository is imported. This method will inspect the list of repositories - about to be exported and make sure to order them appropriately for proper import. For each repository - about to be exported, if required repositories are not contained in the list of repositories about to - be exported, then they are not considered. Repository dependency definitions that contain circular - dependencies should not result in an infinite loop, but obviously ordering the list will not be handled - for one or more of the repositories that require prior import. - """ - # The received primary_repository_id is the id of the repository being exported, with the received list - # of repository_ids being only the ids of all of its repository dependencies. The primary repository will - # always be last in the returned lists. - ordered_repository_ids = [] - ordered_repositories = [] - ordered_changeset_revisions = [] - # Create a dictionary whose keys are the received repository_ids and whose values are a list of - # repository_ids, each of which is contained in the received list of repository_ids and whose associated - # repository must be imported prior to the repository associated with the repository_id key. - prior_import_required_dict = suc.get_prior_import_or_install_required_dict( app, repository_ids, repo_info_dicts ) - processed_repository_ids = [] - # Process the list of repository dependencies defined for the repository associated with the received - # primary_repository_id. - while len( processed_repository_ids ) != len( prior_import_required_dict.keys() ): - repository_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_import_required_dict, processed_repository_ids ) - if repository_id == primary_repository_id: - # Append the primary_repository_id without processing it since it must be returned last in the order. - # It will be processed below after all dependencies are processed. - processed_repository_ids.append( primary_repository_id ) - continue - processed_repository_ids.append( repository_id ) - if repository_id not in ordered_repository_ids: - prior_import_required_ids = prior_import_required_dict[ repository_id ] - for prior_import_required_id in prior_import_required_ids: - if prior_import_required_id not in ordered_repository_ids: - # Import the associated repository dependency first. - prior_repo_info_dict = get_repo_info_dict_for_import( prior_import_required_id, repository_ids, repo_info_dicts ) - prior_repository, prior_import_changeset_revision = get_components_from_repo_info_dict( app, prior_repo_info_dict ) - if prior_repository and prior_import_changeset_revision: - ordered_repository_ids.append( prior_import_required_id ) - ordered_repositories.append( prior_repository ) - ordered_changeset_revisions.append( prior_import_changeset_revision ) - repo_info_dict = get_repo_info_dict_for_import( repository_id, repository_ids, repo_info_dicts ) - repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict ) - if repository and changeset_revision: - ordered_repository_ids.append( repository_id ) - ordered_repositories.append( repository ) - ordered_changeset_revisions.append( changeset_revision ) - # Process the repository associated with the received primary_repository_id last. - repo_info_dict = get_repo_info_dict_for_import( primary_repository_id, repository_ids, repo_info_dicts ) - repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict ) - if repository and changeset_revision: - ordered_repository_ids.append( repository_id ) - ordered_repositories.append( repository ) - ordered_changeset_revisions.append( changeset_revision ) - return ordered_repository_ids, ordered_repositories, ordered_changeset_revisions - -def remove_protocol_from_tool_shed_url( base_url ): - protocol, base = base_url.split( '://' ) - base = base.replace( ':', '_colon_' ) - base = base.rstrip( '/' ) - return base This diff is so big that we needed to truncate the remainder. 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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