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commit/galaxy-central: guerler: Merge
by commits-noreply＠bitbucket.org 07 Feb '14

07 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/086e594d372c/ Changeset: 086e594d372c User: guerler Date: 2014-02-07 06:06:55 Summary: Merge Affected #: 1 file diff -r dc69ee2333c21cdc24d6b5855355fd5a08a8ab53 -r 086e594d372cc58a823f061c3a008a60c0c33472 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -777,7 +777,7 @@ return dict( operation=self.label, id=item.id ) def allowed( self, item ): if self.condition: - return self.condition( item ) + return bool(self.condition( item )) else: return True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Grids: Convert ill defined conditions to boolean
by commits-noreply＠bitbucket.org 07 Feb '14

07 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/deea87095946/ Changeset: deea87095946 Branch: next-stable User: guerler Date: 2014-02-07 06:05:02 Summary: Grids: Convert ill defined conditions to boolean Affected #: 1 file diff -r d5ce503c01b7e5520133014d0927b3d062eb9705 -r deea87095946ea32d28491b44a120bbc94683150 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -768,7 +768,7 @@ return dict( operation=self.label, id=item.id ) def allowed( self, item ): if self.condition: - return self.condition( item ) + return bool(self.condition( item )) else: return True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Add default parameter to quota undelete grid action
by commits-noreply＠bitbucket.org 07 Feb '14

07 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc69ee2333c2/ Changeset: dc69ee2333c2 User: guerler Date: 2014-02-07 04:37:40 Summary: Add default parameter to quota undelete grid action Affected #: 1 file diff -r 4ede9ee8278e18df75a3d79b7a6b133274b058b6 -r dc69ee2333c21cdc24d6b5855355fd5a08a8ab53 lib/galaxy/actions/admin.py --- a/lib/galaxy/actions/admin.py +++ b/lib/galaxy/actions/admin.py @@ -150,7 +150,7 @@ message += ', '.join( names ) return message - def _undelete_quota( self, quota, params ): + def _undelete_quota( self, quota, params = None): quotas = util.listify( quota ) names = [] for q in quotas: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Fix undelete action in quota grid
by commits-noreply＠bitbucket.org 07 Feb '14

07 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ede9ee8278e/ Changeset: 4ede9ee8278e User: guerler Date: 2014-02-07 04:34:44 Summary: Fix undelete action in quota grid Affected #: 1 file diff -r a2739727943039f4c8f74194491396ffa1299267 -r 4ede9ee8278e18df75a3d79b7a6b133274b058b6 lib/galaxy/actions/admin.py --- a/lib/galaxy/actions/admin.py +++ b/lib/galaxy/actions/admin.py @@ -150,7 +150,7 @@ message += ', '.join( names ) return message - def _undelete_quota( self, quota ): + def _undelete_quota( self, quota, params ): quotas = util.listify( quota ) names = [] for q in quotas: 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 07 Feb '14

07 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d5ce503c01b7/ Changeset: d5ce503c01b7 Branch: next-stable User: jeremy goecks Date: 2014-02-07 03:41:32 Summary: Prioritize gene id over transcript id for interval name in GFF data provider. Affected #: 1 file diff -r 54508df431ac564f4ddaf37e3c647f5b18576cbf -r d5ce503c01b7e5520133014d0927b3d062eb9705 lib/galaxy/datatypes/util/gff_util.py --- a/lib/galaxy/datatypes/util/gff_util.py +++ b/lib/galaxy/datatypes/util/gff_util.py @@ -75,7 +75,7 @@ # Preference for name: GTF, GFF3, GFF. for attr_name in [ # GTF: - 'transcript_id', 'gene_id', + 'gene_id', 'transcript_id', # GFF3: 'ID', 'id', # GFF (TODO): https://bitbucket.org/galaxy/galaxy-central/commits/a27397279430/ Changeset: a27397279430 User: jeremy goecks Date: 2014-02-07 03:42:29 Summary: Merge next-stable to default Affected #: 1 file diff -r d92f65506e1cdc46b29aa0049d04bf2fb4179742 -r a2739727943039f4c8f74194491396ffa1299267 lib/galaxy/datatypes/util/gff_util.py --- a/lib/galaxy/datatypes/util/gff_util.py +++ b/lib/galaxy/datatypes/util/gff_util.py @@ -75,7 +75,7 @@ # Preference for name: GTF, GFF3, GFF. for attr_name in [ # GTF: - 'transcript_id', 'gene_id', + 'gene_id', 'transcript_id', # GFF3: 'ID', 'id', # GFF (TODO): 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 06 Feb '14

06 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/54508df431ac/ Changeset: 54508df431ac Branch: next-stable User: jmchilton Date: 2014-02-07 00:08:36 Summary: Fix documentation on normalize remote user e-mail. Listed values should be unmodified defaults. Affected #: 1 file diff -r 0a9053d624bb0bf253b51b99f07cb600b3fb3490 -r 54508df431ac564f4ddaf37e3c647f5b18576cbf universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -602,9 +602,9 @@ #remote_user_logout_href = None # If your proxy and/or authentication source does not normalize e-mail -# addresses or user names being passed to Galaxy - enable the following option -# to force these to lower case. -#normalize_remote_user_email = True +# addresses or user names being passed to Galaxy - set the following option +# to True to force these to lower case. +#normalize_remote_user_email = False # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section https://bitbucket.org/galaxy/galaxy-central/commits/d92f65506e1c/ Changeset: d92f65506e1c User: jmchilton Date: 2014-02-07 00:08:58 Summary: Merge next-stable. Affected #: 1 file diff -r d282cb8daecb0748350a6ea69164071854fdaf60 -r d92f65506e1cdc46b29aa0049d04bf2fb4179742 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -602,9 +602,9 @@ #remote_user_logout_href = None # If your proxy and/or authentication source does not normalize e-mail -# addresses or user names being passed to Galaxy - enable the following option -# to force these to lower case. -#normalize_remote_user_email = True +# addresses or user names being passed to Galaxy - set the following option +# to True to force these to lower case. +#normalize_remote_user_email = False # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section 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 06 Feb '14

06 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a9053d624bb/ Changeset: 0a9053d624bb Branch: next-stable User: carlfeberhard Date: 2014-02-06 22:55:05 Summary: Move misc_info trimming to server side (causing UI flash on updates); Correctly handle wide misc info scrolling Affected #: 5 files diff -r ca4c4a24bd6a853993fc171394c0d2da75fc8829 -r 0a9053d624bb0bf253b51b99f07cb600b3fb3490 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1799,7 +1799,7 @@ update_time = hda.update_time.isoformat(), data_type = hda.ext, genome_build = hda.dbkey, - misc_info = hda.info, + misc_info = hda.info.strip() if isinstance( hda.info, basestring ) else hda.info, misc_blurb = hda.blurb ) # add tags string list diff -r ca4c4a24bd6a853993fc171394c0d2da75fc8829 -r 0a9053d624bb0bf253b51b99f07cb600b3fb3490 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -115,13 +115,6 @@ }, // ........................................................................ common queries - toJSON : function(){ - var json = Backbone.Model.prototype.toJSON.call( this ); - //HACK: this should be done on the server side when setting - json.misc_info = jQuery.trim( json.misc_info ); - return json; - }, - /** Is this hda deleted or purged? */ isDeletedOrPurged : function(){ return ( this.get( 'deleted' ) || this.get( 'purged' ) ); diff -r ca4c4a24bd6a853993fc171394c0d2da75fc8829 -r 0a9053d624bb0bf253b51b99f07cb600b3fb3490 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -define([],function(){var d=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var i=this.get("id");if(!i){return{}}var h={purge:galaxy_config.root+"datasets/"+i+"/purge_async",display:galaxy_config.root+"datasets/"+i+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+i+"/edit",download:galaxy_config.root+"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+i,rerun:galaxy_config.root+"tool_runner/rerun?id="+i,show_params:galaxy_config.root+"datasets/"+i+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+i,set:galaxy_config.root+"dataset/annotate_async?id="+i},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};return h},initialize:function(h){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}})},toJSON:function(){var h=Backbone.Model.prototype.toJSON.call(this);h.misc_info=jQuery.trim(h.misc_info);return h},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(i,j){var h=true;if((!i)&&(this.get("deleted")||this.get("purged"))){h=false}if((!j)&&(!this.get("visible"))){h=false}return h},hidden:function(){return !this.get("visible")},inReadyState:function(){var h=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(h){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},h)},undelete:function a(h){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},h)},hide:function b(h){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},h)},unhide:function g(h){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},h)},purge:function f(h){if(this.get("purged")){return jQuery.when()}h=h||{};h.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set({deleted:true,purged:true})});j.fail(function(o,k,n){var l=_l("Unable to purge dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,_l(l),{error:l})});return j},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},searchAttribute:function(j,h){var i=this.get(j);if(!h||(i===undefined||i===null)){return false}if(_.isArray(i)){return this._searchArrayAttribute(i,h)}return(i.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)},_searchArrayAttribute:function(i,h){h=h.toLowerCase();return _.any(i,function(j){return(j.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)})},search:function(h){var i=this;return _.filter(this.searchAttributes,function(j){return i.searchAttribute(j,h)})},matches:function(i){var k="=",h=i.split(k);if(h.length>=2){var j=h[0];j=this.searchAliases[j]||j;return this.searchAttribute(j,h[1])}return !!this.search(i).length},matchesAll:function(i){var h=this;i=i.match(/(".*"|\w*=".*"|\S*)/g).filter(function(j){return !!j});return _.all(i,function(j){j=j.replace(/"/g,"");return h.matches(j)})},toString:function(){var h=this.get("id")||"";if(this.get("name")){h=this.get("hid")+' :"'+this.get("name")+'",'+h}return"HDA("+h+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.NEW,d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA];var e=Backbone.Collection.extend(LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(i,h){h=h||{};this.historyId=h.historyId},ids:function(){return this.map(function(h){return h.id})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];var i=new e(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new e(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){var m=i.get(l.id);if(!m){return l}var k=m.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryDatasetAssociation:d,HDACollection:e}}); \ No newline at end of file +define([],function(){var d=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var i=this.get("id");if(!i){return{}}var h={purge:galaxy_config.root+"datasets/"+i+"/purge_async",display:galaxy_config.root+"datasets/"+i+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+i+"/edit",download:galaxy_config.root+"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+i,rerun:galaxy_config.root+"tool_runner/rerun?id="+i,show_params:galaxy_config.root+"datasets/"+i+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+i,set:galaxy_config.root+"dataset/annotate_async?id="+i},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};return h},initialize:function(h){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(i,j){var h=true;if((!i)&&(this.get("deleted")||this.get("purged"))){h=false}if((!j)&&(!this.get("visible"))){h=false}return h},hidden:function(){return !this.get("visible")},inReadyState:function(){var h=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(h){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},h)},undelete:function a(h){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},h)},hide:function b(h){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},h)},unhide:function g(h){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},h)},purge:function f(h){if(this.get("purged")){return jQuery.when()}h=h||{};h.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set({deleted:true,purged:true})});j.fail(function(o,k,n){var l=_l("Unable to purge dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,_l(l),{error:l})});return j},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},searchAttribute:function(j,h){var i=this.get(j);if(!h||(i===undefined||i===null)){return false}if(_.isArray(i)){return this._searchArrayAttribute(i,h)}return(i.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)},_searchArrayAttribute:function(i,h){h=h.toLowerCase();return _.any(i,function(j){return(j.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)})},search:function(h){var i=this;return _.filter(this.searchAttributes,function(j){return i.searchAttribute(j,h)})},matches:function(i){var k="=",h=i.split(k);if(h.length>=2){var j=h[0];j=this.searchAliases[j]||j;return this.searchAttribute(j,h[1])}return !!this.search(i).length},matchesAll:function(i){var h=this;i=i.match(/(".*"|\w*=".*"|\S*)/g).filter(function(j){return !!j});return _.all(i,function(j){j=j.replace(/"/g,"");return h.matches(j)})},toString:function(){var h=this.get("id")||"";if(this.get("name")){h=this.get("hid")+' :"'+this.get("name")+'",'+h}return"HDA("+h+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.NEW,d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA];var e=Backbone.Collection.extend(LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(i,h){h=h||{};this.historyId=h.historyId},ids:function(){return this.map(function(h){return h.id})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];var i=new e(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new e(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){var m=i.get(l.id);if(!m){return l}var k=m.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryDatasetAssociation:d,HDACollection:e}}); \ No newline at end of file diff -r ca4c4a24bd6a853993fc171394c0d2da75fc8829 -r 0a9053d624bb0bf253b51b99f07cb600b3fb3490 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1593,7 +1593,7 @@ .history-panel .dataset .dataset-body .dataset-summary .dataset-datatype,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} .history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} .history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} -.history-panel .dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.history-panel .dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} +.history-panel .dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto}.history-panel .dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} .history-panel .dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} .history-panel .dataset .dataset-body .dataset-actions .left{display:inline-block;float:left}.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} .history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} diff -r ca4c4a24bd6a853993fc171394c0d2da75fc8829 -r 0a9053d624bb0bf253b51b99f07cb600b3fb3490 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -216,6 +216,7 @@ } .dataset-info { .info-section; + overflow: auto; .value { white-space: pre-line; } https://bitbucket.org/galaxy/galaxy-central/commits/d282cb8daecb/ Changeset: d282cb8daecb User: carlfeberhard Date: 2014-02-06 22:55:28 Summary: merge Affected #: 5 files diff -r c2fbf6fc1213eda63f56611635857e58388e2f0e -r d282cb8daecb0748350a6ea69164071854fdaf60 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1826,7 +1826,7 @@ update_time = hda.update_time.isoformat(), data_type = hda.ext, genome_build = hda.dbkey, - misc_info = hda.info, + misc_info = hda.info.strip() if isinstance( hda.info, basestring ) else hda.info, misc_blurb = hda.blurb ) # add tags string list diff -r c2fbf6fc1213eda63f56611635857e58388e2f0e -r d282cb8daecb0748350a6ea69164071854fdaf60 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -115,13 +115,6 @@ }, // ........................................................................ common queries - toJSON : function(){ - var json = Backbone.Model.prototype.toJSON.call( this ); - //HACK: this should be done on the server side when setting - json.misc_info = jQuery.trim( json.misc_info ); - return json; - }, - /** Is this hda deleted or purged? */ isDeletedOrPurged : function(){ return ( this.get( 'deleted' ) || this.get( 'purged' ) ); diff -r c2fbf6fc1213eda63f56611635857e58388e2f0e -r d282cb8daecb0748350a6ea69164071854fdaf60 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -define([],function(){var d=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var i=this.get("id");if(!i){return{}}var h={purge:galaxy_config.root+"datasets/"+i+"/purge_async",display:galaxy_config.root+"datasets/"+i+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+i+"/edit",download:galaxy_config.root+"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+i,rerun:galaxy_config.root+"tool_runner/rerun?id="+i,show_params:galaxy_config.root+"datasets/"+i+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+i,set:galaxy_config.root+"dataset/annotate_async?id="+i},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};return h},initialize:function(h){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}})},toJSON:function(){var h=Backbone.Model.prototype.toJSON.call(this);h.misc_info=jQuery.trim(h.misc_info);return h},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(i,j){var h=true;if((!i)&&(this.get("deleted")||this.get("purged"))){h=false}if((!j)&&(!this.get("visible"))){h=false}return h},hidden:function(){return !this.get("visible")},inReadyState:function(){var h=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(h){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},h)},undelete:function a(h){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},h)},hide:function b(h){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},h)},unhide:function g(h){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},h)},purge:function f(h){if(this.get("purged")){return jQuery.when()}h=h||{};h.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set({deleted:true,purged:true})});j.fail(function(o,k,n){var l=_l("Unable to purge dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,_l(l),{error:l})});return j},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},searchAttribute:function(j,h){var i=this.get(j);if(!h||(i===undefined||i===null)){return false}if(_.isArray(i)){return this._searchArrayAttribute(i,h)}return(i.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)},_searchArrayAttribute:function(i,h){h=h.toLowerCase();return _.any(i,function(j){return(j.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)})},search:function(h){var i=this;return _.filter(this.searchAttributes,function(j){return i.searchAttribute(j,h)})},matches:function(i){var k="=",h=i.split(k);if(h.length>=2){var j=h[0];j=this.searchAliases[j]||j;return this.searchAttribute(j,h[1])}return !!this.search(i).length},matchesAll:function(i){var h=this;i=i.match(/(".*"|\w*=".*"|\S*)/g).filter(function(j){return !!j});return _.all(i,function(j){j=j.replace(/"/g,"");return h.matches(j)})},toString:function(){var h=this.get("id")||"";if(this.get("name")){h=this.get("hid")+' :"'+this.get("name")+'",'+h}return"HDA("+h+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.NEW,d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA];var e=Backbone.Collection.extend(LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(i,h){h=h||{};this.historyId=h.historyId},ids:function(){return this.map(function(h){return h.id})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];var i=new e(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new e(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){var m=i.get(l.id);if(!m){return l}var k=m.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryDatasetAssociation:d,HDACollection:e}}); \ No newline at end of file +define([],function(){var d=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var i=this.get("id");if(!i){return{}}var h={purge:galaxy_config.root+"datasets/"+i+"/purge_async",display:galaxy_config.root+"datasets/"+i+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+i+"/edit",download:galaxy_config.root+"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+i,rerun:galaxy_config.root+"tool_runner/rerun?id="+i,show_params:galaxy_config.root+"datasets/"+i+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+i,set:galaxy_config.root+"dataset/annotate_async?id="+i},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};return h},initialize:function(h){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(i,j){var h=true;if((!i)&&(this.get("deleted")||this.get("purged"))){h=false}if((!j)&&(!this.get("visible"))){h=false}return h},hidden:function(){return !this.get("visible")},inReadyState:function(){var h=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(h){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},h)},undelete:function a(h){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},h)},hide:function b(h){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},h)},unhide:function g(h){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},h)},purge:function f(h){if(this.get("purged")){return jQuery.when()}h=h||{};h.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set({deleted:true,purged:true})});j.fail(function(o,k,n){var l=_l("Unable to purge dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,_l(l),{error:l})});return j},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},searchAttribute:function(j,h){var i=this.get(j);if(!h||(i===undefined||i===null)){return false}if(_.isArray(i)){return this._searchArrayAttribute(i,h)}return(i.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)},_searchArrayAttribute:function(i,h){h=h.toLowerCase();return _.any(i,function(j){return(j.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)})},search:function(h){var i=this;return _.filter(this.searchAttributes,function(j){return i.searchAttribute(j,h)})},matches:function(i){var k="=",h=i.split(k);if(h.length>=2){var j=h[0];j=this.searchAliases[j]||j;return this.searchAttribute(j,h[1])}return !!this.search(i).length},matchesAll:function(i){var h=this;i=i.match(/(".*"|\w*=".*"|\S*)/g).filter(function(j){return !!j});return _.all(i,function(j){j=j.replace(/"/g,"");return h.matches(j)})},toString:function(){var h=this.get("id")||"";if(this.get("name")){h=this.get("hid")+' :"'+this.get("name")+'",'+h}return"HDA("+h+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.NEW,d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA];var e=Backbone.Collection.extend(LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(i,h){h=h||{};this.historyId=h.historyId},ids:function(){return this.map(function(h){return h.id})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];var i=new e(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new e(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){var m=i.get(l.id);if(!m){return l}var k=m.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryDatasetAssociation:d,HDACollection:e}}); \ No newline at end of file diff -r c2fbf6fc1213eda63f56611635857e58388e2f0e -r d282cb8daecb0748350a6ea69164071854fdaf60 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1594,7 +1594,7 @@ .history-panel .dataset .dataset-body .dataset-summary .dataset-datatype,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} .history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} .history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} -.history-panel .dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.history-panel .dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} +.history-panel .dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto}.history-panel .dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} .history-panel .dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} .history-panel .dataset .dataset-body .dataset-actions .left{display:inline-block;float:left}.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} .history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} diff -r c2fbf6fc1213eda63f56611635857e58388e2f0e -r d282cb8daecb0748350a6ea69164071854fdaf60 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -216,6 +216,7 @@ } .dataset-info { .info-section; + overflow: auto; .value { white-space: pre-line; } 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: 4 new changesets
by commits-noreply＠bitbucket.org 06 Feb '14

06 Feb '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2b1b1b0ac9f8/ Changeset: 2b1b1b0ac9f8 User: jmchilton Date: 2014-02-05 22:20:31 Summary: Create replacement dict creation in worfklow controllers once. Both recalculated this per step, brings the actual run code closer together - which will make subsequent changeset diff cleaner. Affected #: 2 files diff -r 99beec4c3a338249ab661a7edc3e30ee115486e9 -r 2b1b1b0ac9f8a2f6a452bb41807baac9d3c827ca lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -267,6 +267,9 @@ outputs = util.odict.odict() rval['history'] = trans.security.encode_id(history.id) rval['outputs'] = [] + + replacement_dict = payload.get('replacement_params', {}) + for step in workflow.steps: job = None if step.type == 'tool' or step.type is None: @@ -281,11 +284,9 @@ job, out_data = tool.execute( trans, step.state.inputs, history=history) outputs[ step.id ] = out_data - # Do post-job actions. - replacement_params = payload.get('replacement_params', {}) for pja in step.post_job_actions: if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict=replacement_params) + ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict=replacement_dict) else: job.add_post_job_action(pja) diff -r 99beec4c3a338249ab661a7edc3e30ee115486e9 -r 2b1b1b0ac9f8a2f6a452bb41807baac9d3c827ca lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1373,6 +1373,13 @@ workflow_invocation = model.WorkflowInvocation() workflow_invocation.workflow = workflow outputs = odict() + + # Build replacement dict for this workflow execution. + replacement_dict = {} + for k, v in kwargs.iteritems(): + if k.startswith('wf_parm|'): + replacement_dict[k[8:]] = v + for i, step in enumerate( workflow.steps ): # Execute module job = None @@ -1401,10 +1408,6 @@ # Create new PJA associations with the created job, to be run on completion. # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. - replacement_dict = {} - for k, v in kwargs.iteritems(): - if k.startswith('wf_parm|'): - replacement_dict[k[8:]] = v for pja in step.post_job_actions: if pja.action_type in ActionBox.immediate_actions: ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict) https://bitbucket.org/galaxy/galaxy-central/commits/b8f7b6c1daf3/ Changeset: b8f7b6c1daf3 User: jmchilton Date: 2014-02-05 22:20:31 Summary: Refactor out common code for running workflows. This probably results in some bug fixes for the API workflow running - such as running tools with multiple=true data input parameters. Affected #: 3 files diff -r 2b1b1b0ac9f8a2f6a452bb41807baac9d3c827ca -r b8f7b6c1daf3834b71dfc1fb73b3d8004b924211 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -9,11 +9,10 @@ from galaxy import exceptions from galaxy import util from galaxy import web -from galaxy.tools.parameters import visit_input_values, DataToolParameter from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.workflow.modules import module_factory -from galaxy.jobs.actions.post import ActionBox +from galaxy.workflow.run import invoke log = logging.getLogger(__name__) @@ -237,6 +236,14 @@ rval = {} for step in workflow.steps: step_errors = None + input_connections_by_name = {} + for conn in step.input_connections: + input_name = conn.input_name + if not input_name in input_connections_by_name: + input_connections_by_name[input_name] = [] + input_connections_by_name[input_name].append(conn) + step.input_connections_by_name = input_connections_by_name + if step.type == 'tool' or step.type is None: step.module = module_factory.from_workflow_step( trans, step ) # Check for missing parameters @@ -259,50 +266,30 @@ return "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id step.module = module_factory.from_workflow_step( trans, step ) step.state = step.module.get_runtime_state() - step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) # Run each step, connecting outputs to inputs - workflow_invocation = self.app.model.WorkflowInvocation() - workflow_invocation.workflow = workflow outputs = util.odict.odict() rval['history'] = trans.security.encode_id(history.id) rval['outputs'] = [] replacement_dict = payload.get('replacement_params', {}) + outputs = invoke( + trans=trans, + workflow=workflow, + target_history=history, + replacement_dict=replacement_dict, + ds_map=ds_map, + ) + trans.sa_session.flush() + + # Build legacy output - should probably include more information from + # outputs. for step in workflow.steps: - job = None if step.type == 'tool' or step.type is None: - tool = self.app.toolbox.get_tool( step.tool_id ) + for v in outputs[ step.id ].itervalues(): + rval[ 'outputs' ].append( trans.security.encode_id( v.id ) ) - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ): - if prefixed_name in step.input_connections_by_name: - conn = step.input_connections_by_name[ prefixed_name ] - return outputs[ conn.output_step.id ][ conn.output_name ] - visit_input_values( tool.inputs, step.state.inputs, callback ) - job, out_data = tool.execute( trans, step.state.inputs, history=history) - outputs[ step.id ] = out_data - - for pja in step.post_job_actions: - if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict=replacement_dict) - else: - job.add_post_job_action(pja) - - for v in out_data.itervalues(): - rval['outputs'].append(trans.security.encode_id(v.id)) - else: - #This is an input step. Use the dataset inputs from ds_map. - job, out_data = step.module.execute( trans, step.state) - outputs[step.id] = out_data - outputs[step.id]['output'] = ds_map[str(step.id)]['hda'] - workflow_invocation_step = self.app.model.WorkflowInvocationStep() - workflow_invocation_step.workflow_invocation = workflow_invocation - workflow_invocation_step.workflow_step = step - workflow_invocation_step.job = job - trans.sa_session.add( workflow_invocation ) - trans.sa_session.flush() return rval @web.expose_api diff -r 2b1b1b0ac9f8a2f6a452bb41807baac9d3c827ca -r b8f7b6c1daf3834b71dfc1fb73b3d8004b924211 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -18,7 +18,6 @@ from galaxy import util from galaxy import web from galaxy.datatypes.data import Data -from galaxy.jobs.actions.post import ActionBox from galaxy.model.item_attrs import UsesItemRatings from galaxy.model.mapping import desc from galaxy.tools.parameters import visit_input_values @@ -33,6 +32,7 @@ from galaxy.web.framework.helpers import grids, time_ago from galaxy.web.framework.helpers import to_unicode from galaxy.workflow.modules import module_factory +from galaxy.workflow.run import invoke class StoredWorkflowListGrid( grids.Grid ): @@ -1369,10 +1369,6 @@ target_history = new_history else: target_history = trans.get_history() - # Run each step, connecting outputs to inputs - workflow_invocation = model.WorkflowInvocation() - workflow_invocation.workflow = workflow - outputs = odict() # Build replacement dict for this workflow execution. replacement_dict = {} @@ -1380,54 +1376,14 @@ if k.startswith('wf_parm|'): replacement_dict[k[8:]] = v - for i, step in enumerate( workflow.steps ): - # Execute module - job = None - if step.type == 'tool' or step.type is None: - tool = trans.app.toolbox.get_tool( step.tool_id ) + outputs = invoke( + trans=trans, + workflow=workflow, + target_history=target_history, + replacement_dict=replacement_dict, + copy_inputs_to_history=new_history is not None + ) - # Connect up - def callback( input, value, prefixed_name, prefixed_label ): - replacement = None - if isinstance( input, DataToolParameter ): - if prefixed_name in step.input_connections_by_name: - conn = step.input_connections_by_name[ prefixed_name ] - if input.multiple: - replacement = [outputs[ c.output_step.id ][ c.output_name ] for c in conn] - else: - replacement = outputs[ conn[0].output_step.id ][ conn[0].output_name ] - return replacement - try: - # Replace DummyDatasets with historydatasetassociations - visit_input_values( tool.inputs, step.state.inputs, callback ) - except KeyError, k: - error( "Error due to input mapping of '%s' in '%s'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." % (tool.name, k.message)) - # Execute it - job, out_data = tool.execute( trans, step.state.inputs, history=target_history) - outputs[ step.id ] = out_data - # Create new PJA associations with the created job, to be run on completion. - # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) - # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. - for pja in step.post_job_actions: - if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict) - else: - job.add_post_job_action(pja) - else: - job, out_data = step.module.execute( trans, step.state ) - outputs[ step.id ] = out_data - if new_history: - for input_dataset_hda in out_data.values(): - new_hda = input_dataset_hda.copy( copy_children=True ) - new_history.add_dataset(new_hda) - outputs[ step.id ]['input_ds_copy'] = new_hda - # Record invocation - workflow_invocation_step = model.WorkflowInvocationStep() - workflow_invocation_step.workflow_invocation = workflow_invocation - workflow_invocation_step.workflow_step = step - workflow_invocation_step.job = job - # All jobs ran successfully, so we can save now - trans.sa_session.add( workflow_invocation ) invocations.append({'outputs': outputs, 'new_history': new_history}) trans.sa_session.flush() diff -r 2b1b1b0ac9f8a2f6a452bb41807baac9d3c827ca -r b8f7b6c1daf3834b71dfc1fb73b3d8004b924211 lib/galaxy/workflow/run.py --- /dev/null +++ b/lib/galaxy/workflow/run.py @@ -0,0 +1,108 @@ +from galaxy import model +from galaxy import exceptions + +from galaxy.jobs.actions.post import ActionBox + +from galaxy.tools.parameters.basic import DataToolParameter +from galaxy.tools.parameters import visit_input_values +from galaxy.util.odict import odict + + +def invoke( trans, workflow, target_history, replacement_dict, copy_inputs_to_history=False, ds_map={} ): + """ Run the supplied workflow in the supplied target_history. + """ + return WorkflowInvoker( + trans, + workflow, + target_history, + replacement_dict, + copy_inputs_to_history=copy_inputs_to_history, + ds_map=ds_map, + ).invoke() + + +class WorkflowInvoker( object ): + + def __init__( self, trans, workflow, target_history, replacement_dict, copy_inputs_to_history, ds_map ): + self.trans = trans + self.workflow = workflow + self.target_history = target_history + self.replacement_dict = replacement_dict + self.copy_inputs_to_history = copy_inputs_to_history + self.ds_map = ds_map + + self.outputs = odict() + + def invoke( self ): + workflow_invocation = model.WorkflowInvocation() + workflow_invocation.workflow = self.workflow + + for step in self.workflow.steps: + job = None + job = self._invoke_step( step ) + # Record invocation + workflow_invocation_step = model.WorkflowInvocationStep() + workflow_invocation_step.workflow_invocation = workflow_invocation + workflow_invocation_step.workflow_step = step + workflow_invocation_step.job = job + + # All jobs ran successfully, so we can save now + self.trans.sa_session.add( workflow_invocation ) + + # Not flushing in here, because web controller may create multiple + # invokations. + return self.outputs + + def _invoke_step( self, step ): + trans = self.trans + outputs = self.outputs + target_history = self.target_history + replacement_dict = self.replacement_dict + + if step.type == 'tool' or step.type is None: + tool = trans.app.toolbox.get_tool( step.tool_id ) + + # Connect up + def callback( input, value, prefixed_name, prefixed_label ): + replacement = None + if isinstance( input, DataToolParameter ): + if prefixed_name in step.input_connections_by_name: + conn = step.input_connections_by_name[ prefixed_name ] + if input.multiple: + replacement = [outputs[ c.output_step.id ][ c.output_name ] for c in conn] + else: + replacement = outputs[ conn[0].output_step.id ][ conn[0].output_name ] + return replacement + try: + # Replace DummyDatasets with historydatasetassociations + visit_input_values( tool.inputs, step.state.inputs, callback ) + except KeyError, k: + raise exceptions.MessageException( "Error due to input mapping of '%s' in '%s'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." % (tool.name, k.message)) + # Execute it + job, out_data = tool.execute( trans, step.state.inputs, history=target_history) + outputs[ step.id ] = out_data + # Create new PJA associations with the created job, to be run on completion. + # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) + # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. + for pja in step.post_job_actions: + if pja.action_type in ActionBox.immediate_actions: + ActionBox.execute( trans.app, trans.sa_session, pja, job, replacement_dict ) + else: + job.add_post_job_action(pja) + else: + job, out_data = step.module.execute( trans, step.state ) + outputs[ step.id ] = out_data + + # Web controller may set copy_inputs_to_history, API controller always sets + # ds_map. + if self.copy_inputs_to_history: + for input_dataset_hda in out_data.values(): + new_hda = input_dataset_hda.copy( copy_children=True ) + target_history.add_dataset(new_hda) + outputs[ step.id ]['input_ds_copy'] = new_hda + if self.ds_map: + outputs[step.id]['output'] = self.ds_map[ str( step.id ) ][ 'hda' ] + + return job + +__all__ = [ invoke ] https://bitbucket.org/galaxy/galaxy-central/commits/f263f13f1e6c/ Changeset: f263f13f1e6c User: jmchilton Date: 2014-02-05 22:20:31 Summary: Refactor 2 paths of workflow step invokation into helper functions. Affected #: 1 file diff -r b8f7b6c1daf3834b71dfc1fb73b3d8004b924211 -r f263f13f1e6c52de6f9b2990a9fe60cf1eef714d lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -54,55 +54,66 @@ return self.outputs def _invoke_step( self, step ): - trans = self.trans - outputs = self.outputs - target_history = self.target_history - replacement_dict = self.replacement_dict - if step.type == 'tool' or step.type is None: - tool = trans.app.toolbox.get_tool( step.tool_id ) - - # Connect up - def callback( input, value, prefixed_name, prefixed_label ): - replacement = None - if isinstance( input, DataToolParameter ): - if prefixed_name in step.input_connections_by_name: - conn = step.input_connections_by_name[ prefixed_name ] - if input.multiple: - replacement = [outputs[ c.output_step.id ][ c.output_name ] for c in conn] - else: - replacement = outputs[ conn[0].output_step.id ][ conn[0].output_name ] - return replacement - try: - # Replace DummyDatasets with historydatasetassociations - visit_input_values( tool.inputs, step.state.inputs, callback ) - except KeyError, k: - raise exceptions.MessageException( "Error due to input mapping of '%s' in '%s'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." % (tool.name, k.message)) - # Execute it - job, out_data = tool.execute( trans, step.state.inputs, history=target_history) - outputs[ step.id ] = out_data - # Create new PJA associations with the created job, to be run on completion. - # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) - # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. - for pja in step.post_job_actions: - if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute( trans.app, trans.sa_session, pja, job, replacement_dict ) - else: - job.add_post_job_action(pja) + job = self._execute_tool_step( step ) else: - job, out_data = step.module.execute( trans, step.state ) - outputs[ step.id ] = out_data - - # Web controller may set copy_inputs_to_history, API controller always sets - # ds_map. - if self.copy_inputs_to_history: - for input_dataset_hda in out_data.values(): - new_hda = input_dataset_hda.copy( copy_children=True ) - target_history.add_dataset(new_hda) - outputs[ step.id ]['input_ds_copy'] = new_hda - if self.ds_map: - outputs[step.id]['output'] = self.ds_map[ str( step.id ) ][ 'hda' ] + job = self._execute_input_step( step ) return job + def _execute_tool_step( self, step ): + trans = self.trans + outputs = self.outputs + replacement_dict = self.replacement_dict + + tool = trans.app.toolbox.get_tool( step.tool_id ) + + # Connect up + def callback( input, value, prefixed_name, prefixed_label ): + replacement = None + if isinstance( input, DataToolParameter ): + if prefixed_name in step.input_connections_by_name: + conn = step.input_connections_by_name[ prefixed_name ] + if input.multiple: + replacement = [outputs[ c.output_step.id ][ c.output_name ] for c in conn] + else: + replacement = outputs[ conn[0].output_step.id ][ conn[0].output_name ] + return replacement + try: + # Replace DummyDatasets with historydatasetassociations + visit_input_values( tool.inputs, step.state.inputs, callback ) + except KeyError, k: + raise exceptions.MessageException( "Error due to input mapping of '%s' in '%s'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." % (tool.name, k.message)) + # Execute it + job, out_data = tool.execute( trans, step.state.inputs, history=self.target_history) + outputs[ step.id ] = out_data + # Create new PJA associations with the created job, to be run on completion. + # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) + # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. + for pja in step.post_job_actions: + if pja.action_type in ActionBox.immediate_actions: + ActionBox.execute( trans.app, trans.sa_session, pja, job, replacement_dict ) + else: + job.add_post_job_action(pja) + + return job + + def _execute_input_step( self, step ): + trans = self.trans + outputs = self.outputs + + job, out_data = step.module.execute( trans, step.state ) + outputs[ step.id ] = out_data + + # Web controller may set copy_inputs_to_history, API controller always sets + # ds_map. + if self.copy_inputs_to_history: + for input_dataset_hda in out_data.values(): + new_hda = input_dataset_hda.copy( copy_children=True ) + self.target_history.add_dataset(new_hda) + outputs[ step.id ]['input_ds_copy'] = new_hda + if self.ds_map: + outputs[step.id]['output'] = self.ds_map[ str( step.id ) ][ 'hda' ] + return job + __all__ = [ invoke ] https://bitbucket.org/galaxy/galaxy-central/commits/c2fbf6fc1213/ Changeset: c2fbf6fc1213 User: jmchilton Date: 2014-02-06 22:00:51 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #320) Refactor common workflow run functionality out of controllers Affected #: 3 files diff -r b2206f4ca10f8cec7c37f43f80fc24f0b93b420b -r c2fbf6fc1213eda63f56611635857e58388e2f0e lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -9,11 +9,10 @@ from galaxy import exceptions from galaxy import util from galaxy import web -from galaxy.tools.parameters import visit_input_values, DataToolParameter from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.workflow.modules import module_factory -from galaxy.jobs.actions.post import ActionBox +from galaxy.workflow.run import invoke log = logging.getLogger(__name__) @@ -237,6 +236,14 @@ rval = {} for step in workflow.steps: step_errors = None + input_connections_by_name = {} + for conn in step.input_connections: + input_name = conn.input_name + if not input_name in input_connections_by_name: + input_connections_by_name[input_name] = [] + input_connections_by_name[input_name].append(conn) + step.input_connections_by_name = input_connections_by_name + if step.type == 'tool' or step.type is None: step.module = module_factory.from_workflow_step( trans, step ) # Check for missing parameters @@ -259,49 +266,30 @@ return "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id step.module = module_factory.from_workflow_step( trans, step ) step.state = step.module.get_runtime_state() - step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) # Run each step, connecting outputs to inputs - workflow_invocation = self.app.model.WorkflowInvocation() - workflow_invocation.workflow = workflow outputs = util.odict.odict() rval['history'] = trans.security.encode_id(history.id) rval['outputs'] = [] + + replacement_dict = payload.get('replacement_params', {}) + + outputs = invoke( + trans=trans, + workflow=workflow, + target_history=history, + replacement_dict=replacement_dict, + ds_map=ds_map, + ) + trans.sa_session.flush() + + # Build legacy output - should probably include more information from + # outputs. for step in workflow.steps: - job = None if step.type == 'tool' or step.type is None: - tool = self.app.toolbox.get_tool( step.tool_id ) + for v in outputs[ step.id ].itervalues(): + rval[ 'outputs' ].append( trans.security.encode_id( v.id ) ) - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ): - if prefixed_name in step.input_connections_by_name: - conn = step.input_connections_by_name[ prefixed_name ] - return outputs[ conn.output_step.id ][ conn.output_name ] - visit_input_values( tool.inputs, step.state.inputs, callback ) - job, out_data = tool.execute( trans, step.state.inputs, history=history) - outputs[ step.id ] = out_data - - # Do post-job actions. - replacement_params = payload.get('replacement_params', {}) - for pja in step.post_job_actions: - if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict=replacement_params) - else: - job.add_post_job_action(pja) - - for v in out_data.itervalues(): - rval['outputs'].append(trans.security.encode_id(v.id)) - else: - #This is an input step. Use the dataset inputs from ds_map. - job, out_data = step.module.execute( trans, step.state) - outputs[step.id] = out_data - outputs[step.id]['output'] = ds_map[str(step.id)]['hda'] - workflow_invocation_step = self.app.model.WorkflowInvocationStep() - workflow_invocation_step.workflow_invocation = workflow_invocation - workflow_invocation_step.workflow_step = step - workflow_invocation_step.job = job - trans.sa_session.add( workflow_invocation ) - trans.sa_session.flush() return rval @web.expose_api diff -r b2206f4ca10f8cec7c37f43f80fc24f0b93b420b -r c2fbf6fc1213eda63f56611635857e58388e2f0e lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -18,7 +18,6 @@ from galaxy import util from galaxy import web from galaxy.datatypes.data import Data -from galaxy.jobs.actions.post import ActionBox from galaxy.model.item_attrs import UsesItemRatings from galaxy.model.mapping import desc from galaxy.tools.parameters import visit_input_values @@ -33,6 +32,7 @@ from galaxy.web.framework.helpers import grids, time_ago from galaxy.web.framework.helpers import to_unicode from galaxy.workflow.modules import module_factory +from galaxy.workflow.run import invoke class StoredWorkflowListGrid( grids.Grid ): @@ -1369,62 +1369,21 @@ target_history = new_history else: target_history = trans.get_history() - # Run each step, connecting outputs to inputs - workflow_invocation = model.WorkflowInvocation() - workflow_invocation.workflow = workflow - outputs = odict() - for i, step in enumerate( workflow.steps ): - # Execute module - job = None - if step.type == 'tool' or step.type is None: - tool = trans.app.toolbox.get_tool( step.tool_id ) - # Connect up - def callback( input, value, prefixed_name, prefixed_label ): - replacement = None - if isinstance( input, DataToolParameter ): - if prefixed_name in step.input_connections_by_name: - conn = step.input_connections_by_name[ prefixed_name ] - if input.multiple: - replacement = [outputs[ c.output_step.id ][ c.output_name ] for c in conn] - else: - replacement = outputs[ conn[0].output_step.id ][ conn[0].output_name ] - return replacement - try: - # Replace DummyDatasets with historydatasetassociations - visit_input_values( tool.inputs, step.state.inputs, callback ) - except KeyError, k: - error( "Error due to input mapping of '%s' in '%s'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." % (tool.name, k.message)) - # Execute it - job, out_data = tool.execute( trans, step.state.inputs, history=target_history) - outputs[ step.id ] = out_data - # Create new PJA associations with the created job, to be run on completion. - # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) - # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. - replacement_dict = {} - for k, v in kwargs.iteritems(): - if k.startswith('wf_parm|'): - replacement_dict[k[8:]] = v - for pja in step.post_job_actions: - if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict) - else: - job.add_post_job_action(pja) - else: - job, out_data = step.module.execute( trans, step.state ) - outputs[ step.id ] = out_data - if new_history: - for input_dataset_hda in out_data.values(): - new_hda = input_dataset_hda.copy( copy_children=True ) - new_history.add_dataset(new_hda) - outputs[ step.id ]['input_ds_copy'] = new_hda - # Record invocation - workflow_invocation_step = model.WorkflowInvocationStep() - workflow_invocation_step.workflow_invocation = workflow_invocation - workflow_invocation_step.workflow_step = step - workflow_invocation_step.job = job - # All jobs ran successfully, so we can save now - trans.sa_session.add( workflow_invocation ) + # Build replacement dict for this workflow execution. + replacement_dict = {} + for k, v in kwargs.iteritems(): + if k.startswith('wf_parm|'): + replacement_dict[k[8:]] = v + + outputs = invoke( + trans=trans, + workflow=workflow, + target_history=target_history, + replacement_dict=replacement_dict, + copy_inputs_to_history=new_history is not None + ) + invocations.append({'outputs': outputs, 'new_history': new_history}) trans.sa_session.flush() diff -r b2206f4ca10f8cec7c37f43f80fc24f0b93b420b -r c2fbf6fc1213eda63f56611635857e58388e2f0e lib/galaxy/workflow/run.py --- /dev/null +++ b/lib/galaxy/workflow/run.py @@ -0,0 +1,119 @@ +from galaxy import model +from galaxy import exceptions + +from galaxy.jobs.actions.post import ActionBox + +from galaxy.tools.parameters.basic import DataToolParameter +from galaxy.tools.parameters import visit_input_values +from galaxy.util.odict import odict + + +def invoke( trans, workflow, target_history, replacement_dict, copy_inputs_to_history=False, ds_map={} ): + """ Run the supplied workflow in the supplied target_history. + """ + return WorkflowInvoker( + trans, + workflow, + target_history, + replacement_dict, + copy_inputs_to_history=copy_inputs_to_history, + ds_map=ds_map, + ).invoke() + + +class WorkflowInvoker( object ): + + def __init__( self, trans, workflow, target_history, replacement_dict, copy_inputs_to_history, ds_map ): + self.trans = trans + self.workflow = workflow + self.target_history = target_history + self.replacement_dict = replacement_dict + self.copy_inputs_to_history = copy_inputs_to_history + self.ds_map = ds_map + + self.outputs = odict() + + def invoke( self ): + workflow_invocation = model.WorkflowInvocation() + workflow_invocation.workflow = self.workflow + + for step in self.workflow.steps: + job = None + job = self._invoke_step( step ) + # Record invocation + workflow_invocation_step = model.WorkflowInvocationStep() + workflow_invocation_step.workflow_invocation = workflow_invocation + workflow_invocation_step.workflow_step = step + workflow_invocation_step.job = job + + # All jobs ran successfully, so we can save now + self.trans.sa_session.add( workflow_invocation ) + + # Not flushing in here, because web controller may create multiple + # invokations. + return self.outputs + + def _invoke_step( self, step ): + if step.type == 'tool' or step.type is None: + job = self._execute_tool_step( step ) + else: + job = self._execute_input_step( step ) + + return job + + def _execute_tool_step( self, step ): + trans = self.trans + outputs = self.outputs + replacement_dict = self.replacement_dict + + tool = trans.app.toolbox.get_tool( step.tool_id ) + + # Connect up + def callback( input, value, prefixed_name, prefixed_label ): + replacement = None + if isinstance( input, DataToolParameter ): + if prefixed_name in step.input_connections_by_name: + conn = step.input_connections_by_name[ prefixed_name ] + if input.multiple: + replacement = [outputs[ c.output_step.id ][ c.output_name ] for c in conn] + else: + replacement = outputs[ conn[0].output_step.id ][ conn[0].output_name ] + return replacement + try: + # Replace DummyDatasets with historydatasetassociations + visit_input_values( tool.inputs, step.state.inputs, callback ) + except KeyError, k: + raise exceptions.MessageException( "Error due to input mapping of '%s' in '%s'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." % (tool.name, k.message)) + # Execute it + job, out_data = tool.execute( trans, step.state.inputs, history=self.target_history) + outputs[ step.id ] = out_data + # Create new PJA associations with the created job, to be run on completion. + # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) + # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. + for pja in step.post_job_actions: + if pja.action_type in ActionBox.immediate_actions: + ActionBox.execute( trans.app, trans.sa_session, pja, job, replacement_dict ) + else: + job.add_post_job_action(pja) + + return job + + def _execute_input_step( self, step ): + trans = self.trans + outputs = self.outputs + + job, out_data = step.module.execute( trans, step.state ) + outputs[ step.id ] = out_data + + # Web controller may set copy_inputs_to_history, API controller always sets + # ds_map. + if self.copy_inputs_to_history: + for input_dataset_hda in out_data.values(): + new_hda = input_dataset_hda.copy( copy_children=True ) + self.target_history.add_dataset(new_hda) + outputs[ step.id ]['input_ds_copy'] = new_hda + if self.ds_map: + outputs[step.id]['output'] = self.ds_map[ str( step.id ) ][ 'hda' ] + return job + +__all__ = [ invoke ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jeremy goecks: (1) Update Backbone Config objects and (2) add config options to Circster.
by commits-noreply＠bitbucket.org 06 Feb '14

06 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b2206f4ca10f/ Changeset: b2206f4ca10f User: jeremy goecks Date: 2014-02-06 21:41:05 Summary: (1) Update Backbone Config objects and (2) add config options to Circster. Affected #: 4 files diff -r c6eac0859bf917c176ec5995bff92a25841a9420 -r b2206f4ca10f8cec7c37f43f80fc24f0b93b420b static/scripts/packed/utils/config.js --- a/static/scripts/packed/utils/config.js +++ b/static/scripts/packed/utils/config.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util"],function(b,e){var c=Backbone.Model.extend({initialize:function(f){var g=this.get("key");this.set("id",g);var h=b.find(c.known_settings_defaults,function(i){return i.key===g});if(h){this.set(b.extend({},h,f))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",e.get_random_color())}this.on("change:value",this.cast_value,this)},cast_value:function(){var f=this.get("type"),g=this.get("value");if(f==="float"){g=parseFloat(g)}else{if(f==="int"){g=parseInt(g,10)}}this.set("value")}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var f={};this.each(function(g){f[g.get("key")]=g.get("value")});return f},get_value:function(f){var g=this.get(f);if(g){return g.get("value")}return undefined}},{from_config_dict:function(g){var f=b.map(b.keys(g),function(h){return{key:h,value:g[h]}});return new d(f)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var i=this.model;var f=this.$el;var h;function g(n,j){for(var r=0;r<n.length;r++){h=n[r];if(h.hidden){continue}var l="param_"+r;var v=i.values[h.key];var x=$("<div class='form-row' />").appendTo(j);x.append($("<label />").attr("for",l).text(h.label+":"));if(type==="bool"){x.append($('<input type="checkbox" />').attr("id",l).attr("name",l).attr("checked",v))}else{if(type==="text"){x.append($('<input type="text"/>').attr("id",l).val(v).click(function(){$(this).select()}))}else{if(type==="select"){var t=$("<select />").attr("id",l);for(var p=0;p<h.options.length;p++){$("<option/>").text(h.options[p].label).attr("value",h.options[p].value).appendTo(t)}t.val(v);x.append(t)}else{if(type==="color"){var w=$("<div/>").appendTo(x),s=$("<input />").attr("id",l).attr("name",l).val(v).css("float","left").appendTo(w).click(function(z){$(".tooltip").removeClass("in");var y=$(this).siblings(".tooltip").addClass("in");y.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(y).height()/2)+($(this).height()/2)}).show();y.click(function(A){A.stopPropagation()});$(document).bind("click.color-picker",function(){y.hide();$(document).unbind("click.color-picker")});z.stopPropagation()}),q=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(w).attr("title","Set new random color").tooltip(),u=$("<div class='tooltip right' style='position: absolute;' />").appendTo(w).hide(),m=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(u),k=$("<div class='tooltip-arrow'></div>").appendTo(u),o=$.farbtastic(m,{width:100,height:100,callback:s,color:v});w.append($("<div/>").css("clear","both"));(function(y){q.click(function(){y.setColor(e.get_random_color())})})(o)}else{x.append($("<input />").attr("id",l).attr("name",l).val(v))}}}}if(h.help){x.append($("<div class='help'/>").text(h.help))}}}g(this.params,f);return this},render_in_modal:function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){this.update_from_form();hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(i){if((i.keyCode||i.which)===27){h()}else{if((i.keyCode||i.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:"Configure",body:drawable.config.build_form(),buttons:{Cancel:h,OK:f}})},update_from_form:function(){var f=this;this.collection.each(function(h,g){if(!h.get("hidden")){var j="param_"+g;var i=f.$el.find("#"+j).val();if(type==="bool"){i=container.find("#"+j).is(":checked")}h.set("value",i)}})}});return{ConfigSettingCollection:d,ConfigSettingCollectionView:a}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",f.get_random_color())}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined}},{from_config_dict:function(h){var g=c.map(c.keys(h),function(i){return{key:i,value:h[i]}});return new e(g)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(k,p){if(k.get("hidden")){return}var j="param_"+p,q=k.get("type"),u=k.get("value");var w=$("<div class='form-row' />").appendTo(g);w.append($("<label />").attr("for",j).text(k.get("label")+":"));if(q==="bool"){w.append($('<input type="checkbox" />').attr("id",j).attr("name",j).attr("checked",u))}else{if(q==="text"){w.append($('<input type="text"/>').attr("id",j).val(u).click(function(){$(this).select()}))}else{if(q==="select"){var s=$("<select />").attr("id",j);for(var n=0;n<k.options.length;n++){$("<option/>").text(k.options[n].label).attr("value",k.options[n].value).appendTo(s)}s.val(u);w.append(s)}else{if(q==="color"){var v=$("<div/>").appendTo(w),r=$("<input />").attr("id",j).attr("name",j).val(u).css("float","left").appendTo(v).click(function(x){$(".tooltip").removeClass("in");var i=$(this).siblings(".tooltip").addClass("in");i.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(i).height()/2)+($(this).height()/2)}).show();i.click(function(y){y.stopPropagation()});$(document).bind("click.color-picker",function(){i.hide();$(document).unbind("click.color-picker")});x.stopPropagation()}),o=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(v).attr("title","Set new random color").tooltip(),t=$("<div class='tooltip right' style='position: absolute;' />").appendTo(v).hide(),l=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(t),h=$("<div class='tooltip-arrow'></div>").appendTo(t),m=$.farbtastic(l,{width:100,height:100,callback:r,color:u});v.append($("<div/>").css("clear","both"));(function(i){o.click(function(){i.setColor(f.get_random_color())})})(m)}else{w.append($("<input />").attr("id",j).attr("name",j).val(u))}}}}if(k.help){w.append($("<div class='help'/>").text(k.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){g.update_from_form();Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=container.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file diff -r c6eac0859bf917c176ec5995bff92a25841a9420 -r b2206f4ca10f8cec7c37f43f80fc24f0b93b420b static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["utils/utils","libs/underscore","libs/d3","viz/visualization"],function(g,h,m,j){g.cssLoadFile("static/style/circster.css");var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(p<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.total_gap=o.total_gap;this.genome=o.genome;this.dataset_arc_height=o.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("drawables").on("add",this.add_track,this);this.model.get("drawables").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var p=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-p.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=m.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var o=this;return h.map(tracks_start_radii,function(q){return[q,q+o.dataset_arc_height]})},render:function(){var x=this,r=this.dataset_arc_height,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),q=this.get_chord_tracks(),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new d({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:x.total_gap});y.render();return y});this.chords_views=q.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:x.total_gap});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new c(),radius_bounds:u,genome:x.genome,total_gap:x.total_gap});this.label_track_view.render()},add_track:function(u){if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:this.total_gap});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new d({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:this.total_gap});o.render();this.circular_views.push(o);var p=s[s.length-1];p[1]=p[0];this.label_track_view.update_radius_bounds(p)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;if(!s){console.log("no parent elt")}var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){var t=h.reject(h.map(u,function(v,w){var x=null,y=q._get_path_function(r[w],v);if(y){x=y(v.data)}return x}),function(v){return v===null});o.each(function(w,v){m.select(this).transition().duration(1000).attr("d",t[v])})})}},_transition_labels:function(){},_update_data_bounds:function(){var o=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<o[0]||this.data_bounds[1]>o[1]){this._transition_chrom_data()}},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var f=l.extend({_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,p=function(){return"rotate(90)"};this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),p,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(f.prototype,i);var d=f.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var e=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config),r=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.4,genome:o,model:p,dataset_arc_height:25});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:p.get("vis_id"),title:p.get("title"),dbkey:p.get("dbkey"),type:"trackster",vis_json:JSON.stringify(p)}}).success(function(s){Galaxy.modal.hide();p.set("vis_id",s.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file +define(["utils/utils","libs/underscore","libs/d3","viz/visualization","utils/config"],function(h,i,n,k,c){h.cssLoadFile("static/style/circster.css");var o=Backbone.Model.extend({is_visible:function(s,p){var q=s.getBoundingClientRect(),r=$("svg")[0].getBoundingClientRect();if(q.right<0||q.left>r.right||q.bottom<0||q.top>r.bottom){return false}return true}});var j={drawTicks:function(t,s,x,r,p){var w=t.append("g").selectAll("g").data(s).enter().append("g").selectAll("g").data(x).enter().append("g").attr("class","tick").attr("transform",function(y){return"rotate("+(y.angle*180/Math.PI-90)+")translate("+y.radius+",0)"});var v=[],u=[],q=function(y){return y.angle>Math.PI?"end":null};if(p){v=[0,0,0,-4];u=[4,0,"",".35em"];q=null}else{v=[1,0,4,0];u=[0,4,".35em",""]}w.append("line").attr("x1",v[0]).attr("y1",v[1]).attr("x2",v[2]).attr("y1",v[3]).style("stroke","#000");w.append("text").attr("x",u[0]).attr("y",u[1]).attr("dx",u[2]).attr("dy",u[3]).attr("text-anchor",q).attr("transform",r).text(function(y){return y.label})},formatNum:function(q,p){if(p===undefined){p=2}if(q===null){return null}var s=null;if(q<1){s=q.toPrecision(p)}else{var r=Math.round(q.toPrecision(p));if(q<1000){s=r}else{if(q<1000000){s=Math.round((r/1000).toPrecision(3)).toFixed(0)+"K"}else{if(q<1000000000){s=Math.round((r/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return s}};var d=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(p){this.genome=p.genome;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("drawables").on("add",this.add_track,this);this.model.get("drawables").on("remove",this.remove_track,this);var q=this.model.get("config");q.get("arc_dataset_height").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(p){return p.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(p){return p.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var r=this.get_circular_tracks(),s=this.model.get("config").get_value("arc_dataset_height"),p=Math.min(this.$el.width(),this.$el.height()),u=p/2-r.length*(s+this.track_gap)-(this.label_arc_height+this.track_gap),t=n.range(u,p/2,s+this.track_gap);var q=this;return i.map(t,function(v){return[v,v+s]})},render:function(){var y=this,p=y.$el.width(),x=y.$el.height(),u=this.get_circular_tracks(),s=this.get_chord_tracks(),r=y.model.get("config").get_value("total_gap"),t=this.get_tracks_bounds(),q=n.select(y.$el[0]).append("svg").attr("width",p).attr("height",x).attr("pointer-events","all").append("svg:g").call(n.behavior.zoom().on("zoom",function(){var z=n.event.scale;q.attr("transform","translate("+n.event.translate+") scale("+z+")");if(y.scale!==z){if(y.zoom_drag_timeout){clearTimeout(y.zoom_drag_timeout)}y.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+p/2+","+x/2+")").append("svg:g").attr("class","tracks");this.circular_views=u.map(function(A,B){var z=new e({el:q.append("g")[0],track:A,radius_bounds:t[B],genome:y.genome,total_gap:r});z.render();return z});this.chords_views=s.map(function(A){var z=new l({el:q.append("g")[0],track:A,radius_bounds:t[0],genome:y.genome,total_gap:r});z.render();return z});var w=this.circular_views[this.circular_views.length-1].radius_bounds[1],v=[w,w+this.label_arc_height];this.label_track_view=new b({el:q.append("g")[0],track:new d(),radius_bounds:v,genome:y.genome,total_gap:r});this.label_track_view.render()},add_track:function(w){var q=this.model.get("config").get_value("total_gap");if(w.get("track_type")==="DiagonalHeatmapTrack"){var s=this.circular_views[0].radius_bounds,v=new l({el:n.select("g.tracks").append("g")[0],track:w,radius_bounds:s,genome:this.genome,total_gap:q});v.render();this.chords_views.push(v)}else{var u=this.get_tracks_bounds();i.each(this.circular_views,function(x,y){x.update_radius_bounds(u[y])});i.each(this.chords_views,function(x){x.update_radius_bounds(u[0])});var t=this.circular_views.length,p=new e({el:n.select("g.tracks").append("g")[0],track:w,radius_bounds:u[t],genome:this.genome,total_gap:q});p.render();this.circular_views.push(p);var r=u[u.length-1];r[1]=r[0];this.label_track_view.update_radius_bounds(r)}},remove_track:function(q,s,r){var p=this.circular_views[r.index];this.circular_views.splice(r.index,1);p.$el.remove();var t=this.get_tracks_bounds();i.each(this.circular_views,function(u,v){u.update_radius_bounds(t[v])})},update_track_bounds:function(){var p=this.get_tracks_bounds();i.each(this.circular_views,function(q,r){q.update_radius_bounds(p[r])})}});var m=Backbone.View.extend({tagName:"g",initialize:function(p){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=p.total_gap;this.track=p.track;this.radius_bounds=p.radius_bounds;this.genome=p.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=n.select(this.$el[0])},get_fill_color:function(){var p=this.track.get("config").get_value("block_color");if(!p){p=this.track.get("config").get_value("color")}return p},render:function(){var t=this.parent_elt;if(!t){console.log("no parent elt")}var s=this.chroms_layout,v=n.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),p=t.selectAll("g").data(s).enter().append("svg:g"),r=p.append("path").attr("d",v).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);r.append("title").text(function(x){return x.data.chrom});var q=this,u=q.track.get("data_manager"),w=(u?u.data_is_ready():true);$.when(w).then(function(){$.when(q._render_data(t)).then(function(){r.style("fill",q.bg_fill);q.render_labels()})})},render_labels:function(){},update_radius_bounds:function(q){this.radius_bounds=q;var p=n.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",p);this._transition_chrom_data();this._transition_labels()},update_scale:function(s){var r=this.scale;this.scale=s;if(s<=r){return}var q=this,p=new o();this.parent_elt.selectAll("path.chrom-data").filter(function(u,t){return p.is_visible(this)}).each(function(z,v){var y=n.select(this),u=y.attr("chrom"),x=q.genome.get_chrom_region(u),w=q.track.get("data_manager"),t;if(!w.can_get_more_detailed_data(x)){return}t=q.track.get("data_manager").get_more_detailed_data(x,"Coverage",0,s);$.when(t).then(function(C){y.remove();q._update_data_bounds();var B=i.find(q.chroms_layout,function(D){return D.data.chrom===u});var A=q.get_fill_color();q._render_chrom_data(q.parent_elt,B,C).style("stroke",A).style("fill",A)})});return q},_transition_chrom_data:function(){var q=this.track,s=this.chroms_layout,p=this.parent_elt.selectAll("g>path.chrom-data"),t=p[0].length;if(t>0){var r=this;$.when(q.get("data_manager").get_genome_wide_data(this.genome)).then(function(v){var u=i.reject(i.map(v,function(w,x){var y=null,z=r._get_path_function(s[x],w);if(z){y=z(w.data)}return y}),function(w){return w===null});p.each(function(x,w){n.select(this).transition().duration(1000).attr("d",u[w])})})}},_transition_labels:function(){},_update_data_bounds:function(){var p=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<p[0]||this.data_bounds[1]>p[1]){this._transition_chrom_data()}},_render_data:function(s){var r=this,q=this.chroms_layout,p=this.track,t=$.Deferred();$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(v){r.data_bounds=r.get_data_bounds(v);layout_and_data=i.zip(q,v),chroms_data_layout=i.map(layout_and_data,function(w){var x=w[0],y=w[1];return r._render_chrom_data(s,x,y)});var u=r.get_fill_color();r.parent_elt.selectAll("path.chrom-data").style("stroke",u).style("fill",u);t.resolve(s)});return t},_render_chrom_data:function(p,q,r){},_get_path_function:function(q,p){},_chroms_layout:function(){var q=this.genome.get_chroms_info(),s=n.layout.pie().value(function(u){return u.len}).sort(null),t=s(q),p=2*Math.PI*this.total_gap/q.length,r=i.map(t,function(w,v){var u=w.endAngle-p;w.endAngle=(u>w.startAngle?u:w.startAngle);return w});return r}});var b=m.extend({initialize:function(p){m.prototype.initialize.call(this,p);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(r){var q=this,p=r.selectAll("g");p.selectAll("path").attr("id",function(v){return"label-"+v.data.chrom});p.append("svg:text").filter(function(v){return v.endAngle-v.startAngle>q.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(v){return"#label-"+v.data.chrom}).attr("startOffset","25%").text(function(v){return v.data.chrom});var s=function(x){var v=(x.endAngle-x.startAngle)/x.value,w=n.range(0,x.value,25000000).map(function(y,z){return{radius:q.innerRadius,angle:y*v+x.startAngle,label:z===0?0:(z%3?null:q.formatNum(y))}});if(w.length<4){w[w.length-1].label=q.formatNum(Math.round((w[w.length-1].angle-x.startAngle)/v))}return w};var u=function(v){return v.angle>Math.PI?"rotate(180)translate(-16)":null};var t=i.filter(this.chroms_layout,function(v){return v.endAngle-v.startAngle>q.min_arc_len});this.drawTicks(this.parent_elt,t,s,u)}});i.extend(b.prototype,j);var g=m.extend({_quantile:function(q,p){q.sort(n.ascending);return n.quantile(q,p)},_render_chrom_data:function(p,s,q){var t=this._get_path_function(s,q);if(!t){return null}var r=p.datum(q.data),u=r.append("path").attr("class","chrom-data").attr("chrom",s.data.chrom).attr("d",t);return u},_get_path_function:function(s,r){if(typeof r==="string"||!r.data||r.data.length===0){return null}var p=n.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var t=n.scale.linear().domain([0,r.data.length]).range([s.startAngle,s.endAngle]);var q=n.svg.line.radial().interpolate("linear").radius(function(u){return p(u[1])}).angle(function(v,u){return t(u)});return n.svg.area.radial().interpolate(q.interpolate()).innerRadius(p(0)).outerRadius(q.radius()).angle(q.angle())},render_labels:function(){var p=this,q=function(){return"rotate(90)"};this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var q=this,s=i.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>0.08}),r=i.filter(s,function(u,t){return t%3===0}),p=i.flatten(i.map(r,function(t){return q._data_bounds_ticks_fn()(t)}));this.parent_elt.selectAll("g.tick").data(p).transition().attr("transform",function(t){return"rotate("+(t.angle*180/Math.PI-90)+")translate("+t.radius+",0)"})},_data_bounds_ticks_fn:function(){var p=this;visibleChroms=0;return function(q){return[{radius:p.radius_bounds[0],angle:q.startAngle,label:p.formatNum(p.data_bounds[0])},{radius:p.radius_bounds[1],angle:q.startAngle,label:p.formatNum(p.data_bounds[1])}]}},get_data_bounds:function(p){}});i.extend(g.prototype,j);var e=g.extend({get_data_bounds:function(q){var p=i.flatten(i.map(q,function(r){if(r){return i.map(r.data,function(s){return parseInt(s[1],10)||0})}else{return 0}}));return[i.min(p),this._quantile(p,0.98)||i.max(p)]}});var l=m.extend({render:function(){var p=this;$.when(p.track.get("data_manager").data_is_ready()).then(function(){$.when(p.track.get("data_manager").get_genome_wide_data(p.genome)).then(function(s){var r=[],q=p.genome.get_chroms_info();i.each(s,function(w,v){var t=q[v].chrom;var u=i.map(w.data,function(y){var x=p._get_region_angle(t,y[1]),z=p._get_region_angle(y[3],y[4]);return{source:{startAngle:x,endAngle:x+0.01},target:{startAngle:z,endAngle:z+0.01}}});r=r.concat(u)});p.parent_elt.append("g").attr("class","chord").selectAll("path").data(r).enter().append("path").style("fill",p.get_fill_color()).attr("d",n.svg.chord().radius(p.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(p){this.radius_bounds=p;this.parent_elt.selectAll("path").transition().attr("d",n.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(r,p){var q=i.find(this.chroms_layout,function(s){return s.data.chrom===r});return q.endAngle-((q.endAngle-q.startAngle)*(q.data.len-p)/q.data.len)}});var f=Backbone.View.extend({initialize:function(){var p=new k.Genome(galaxy_config.app.genome),q=new k.GenomeVisualization(galaxy_config.app.viz_config);q.get("config").add([{key:"arc_dataset_height",label:"Arc Dataset Height",type:"int",value:25,view:"circster"},{key:"total_gap",label:"Gap [0-1]",type:"float",value:0.4,view:"circster",hidden:true}]);var s=new a({el:$("#center .unified-panel-body"),genome:p,model:q});s.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var r=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){k.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",q.get("dbkey"),function(t){q.add_tracks(t)})}},{icon_class:"gear",title:"Settings",on_click:function(){var t=new c.ConfigSettingCollectionView({collection:q.get("config")});t.render_in_modal("Configure Visualization")}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:q.get("vis_id"),title:q.get("title"),dbkey:q.get("dbkey"),type:"trackster",vis_json:JSON.stringify(q)}}).success(function(t){Galaxy.modal.hide();q.set("vis_id",t.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});r.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(r.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:f}}); \ No newline at end of file diff -r c6eac0859bf917c176ec5995bff92a25841a9420 -r b2206f4ca10f8cec7c37f43f80fc24f0b93b420b static/scripts/utils/config.js --- a/static/scripts/utils/config.js +++ b/static/scripts/utils/config.js @@ -1,9 +1,10 @@ -define(['libs/underscore', 'viz/trackster/util'], function(_, util_mod) { +define(['libs/underscore', 'viz/trackster/util', 'utils/config'], function(_, util_mod, config_mod) { /** * A configuration setting. Currently key is used as id. */ var ConfigSetting = Backbone.Model.extend({ + initialize: function(options) { // Use key as id for now. var key = this.get('key'); @@ -19,26 +20,24 @@ if (this.get('type') === 'color' && !this.get('value')) { this.set('value', util_mod.get_random_color()); } - - // When value updated, cast is appropriately. - this.on('change:value', this.cast_value, this); }, /** - * Cast value from string to appropriate type. + * Cast and set value. This should be instead of + * setting.set('value', new_value) */ - cast_value: function() { - var type = this.get('type'), - value = this.get('value'); + set_value: function(value) { + var type = this.get('type'); if (type === 'float') { - value = parseFloat( value ); - } else if (type === 'int') { - value = parseInt( value, 10 ); + value = parseFloat(value); + } + else if (type === 'int') { + value = parseInt(value, 10); } // TODO: handle casting from string to bool? - this.set('value'); + this.set('value', value); } }, { // This is a master list of default settings for known settings. @@ -92,7 +91,8 @@ return undefined; } -}, { +}, +{ /** * Utility function that creates a ConfigSettingsCollection from a standard dictionary * with configuration key-value pairs. @@ -120,101 +120,99 @@ * Renders form for editing configuration settings. */ render: function() { - var track_config = this.model; var container = this.$el; - var param; + + this.collection.each(function(param, index) { + // Hidden params have no representation in the form + if (param.get('hidden')) { return; } - // Function to process parameters recursively - function handle_params( params, container ) { - for ( var index = 0; index < params.length; index++ ) { - param = params[index]; - // Hidden params have no representation in the form - if ( param.hidden ) { continue; } - // Build row for param - var id = 'param_' + index; - var value = track_config.values[ param.key ]; - var row = $("<div class='form-row' />").appendTo( container ); - row.append( $('<label />').attr("for", id ).text( param.label + ":" ) ); - // Draw parameter as checkbox - if ( type === 'bool' ) { - row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) ); - // Draw parameter as textbox - } else if ( type === 'text' ) { - row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select(); })); - // Draw paramter as select area - } else if ( type === 'select' ) { - var select = $('<select />').attr("id", id); - for ( var i = 0; i < param.options.length; i++ ) { - $("<option/>").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select ); - } - select.val( value ); - row.append( select ); - // Draw parameter as color picker - } else if ( type === 'color' ) { - var - container_div = $("<div/>").appendTo(row), - input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left") - .appendTo(container_div).click(function(e) { - // Hide other pickers. - $(".tooltip").removeClass( "in" ); + // Build row for param. + var id = 'param_' + index, + type = param.get('type'), + value = param.get('value'); + var row = $("<div class='form-row' />").appendTo(container); + row.append($('<label />').attr("for", id ).text(param.get('label') + ":" )); + // Draw parameter as checkbox + if ( type === 'bool' ) { + row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) ); + } + // Draw parameter as textbox + else if ( type === 'text' ) { + row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select(); })); + } + // Draw parameter as select area + else if ( type === 'select' ) { + var select = $('<select />').attr("id", id); + for ( var i = 0; i < param.options.length; i++ ) { + $("<option/>").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select ); + } + select.val( value ); + row.append( select ); + + } + // Draw parameter as color picker + else if ( type === 'color' ) { + var + container_div = $("<div/>").appendTo(row), + input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left") + .appendTo(container_div).click(function(e) { + // Hide other pickers. + $(".tooltip").removeClass( "in" ); + + // Show input's color picker. + var tip = $(this).siblings(".tooltip").addClass( "in" ); + tip.css( { + // left: $(this).position().left + ( $(input).width() / 2 ) - 60, + // top: $(this).position().top + $(this.height) + left: $(this).position().left + $(this).width() + 5, + top: $(this).position().top - ( $(tip).height() / 2 ) + ( $(this).height() / 2 ) + } ).show(); - // Show input's color picker. - var tip = $(this).siblings(".tooltip").addClass( "in" ); - tip.css( { - // left: $(this).position().left + ( $(input).width() / 2 ) - 60, - // top: $(this).position().top + $(this.height) - left: $(this).position().left + $(this).width() + 5, - top: $(this).position().top - ( $(tip).height() / 2 ) + ( $(this).height() / 2 ) - } ).show(); - - // Click management: - - // Keep showing tip if clicking in tip. - tip.click(function(e) { - e.stopPropagation(); - }); - - // Hide tip if clicking outside of tip. - $(document).bind( "click.color-picker", function() { - tip.hide(); - $(document).unbind( "click.color-picker" ); - }); - - // No propagation to avoid triggering document click (and tip hiding) above. + // Click management: + + // Keep showing tip if clicking in tip. + tip.click(function(e) { e.stopPropagation(); - }), - // Icon for setting a new random color; behavior set below. - new_color_icon = $("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(container_div) - .attr("title", "Set new random color").tooltip(), - // Color picker in tool tip style. - tip = $( "<div class='tooltip right' style='position: absolute;' />" ).appendTo(container_div).hide(), - // Inner div for padding purposes - tip_inner = $("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(tip), - tip_arrow = $("<div class='tooltip-arrow'></div>").appendTo(tip), - farb_obj = $.farbtastic(tip_inner, { width: 100, height: 100, callback: input, color: value }); - - // Clear floating. - container_div.append( $("<div/>").css("clear", "both")); - - // Use function to fix farb_obj value. - (function(fixed_farb_obj) { - new_color_icon.click(function() { - fixed_farb_obj.setColor(util_mod.get_random_color()); - }); - })(farb_obj); - - } - else { - row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) ); - } - // Help text - if ( param.help ) { - row.append( $("<div class='help'/>").text( param.help ) ); - } + }); + + // Hide tip if clicking outside of tip. + $(document).bind( "click.color-picker", function() { + tip.hide(); + $(document).unbind( "click.color-picker" ); + }); + + // No propagation to avoid triggering document click (and tip hiding) above. + e.stopPropagation(); + }), + // Icon for setting a new random color; behavior set below. + new_color_icon = $("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(container_div) + .attr("title", "Set new random color").tooltip(), + // Color picker in tool tip style. + tip = $( "<div class='tooltip right' style='position: absolute;' />" ).appendTo(container_div).hide(), + // Inner div for padding purposes + tip_inner = $("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(tip), + tip_arrow = $("<div class='tooltip-arrow'></div>").appendTo(tip), + farb_obj = $.farbtastic(tip_inner, { width: 100, height: 100, callback: input, color: value }); + + // Clear floating. + container_div.append( $("<div/>").css("clear", "both")); + + // Use function to fix farb_obj value. + (function(fixed_farb_obj) { + new_color_icon.click(function() { + fixed_farb_obj.setColor(util_mod.get_random_color()); + }); + })(farb_obj); + + } + else { + row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) ); } - } - // Handle top level parameters in order - handle_params( this.params, container ); + // Help text + if ( param.help ) { + row.append( $("<div class='help'/>").text( param.help ) ); + } + }); return this; }, @@ -222,13 +220,14 @@ /** * Render view in modal. */ - render_in_modal: function() { + render_in_modal: function(title) { // Set up handlers for cancel, ok button and for handling esc key. - var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, + var self = this, + cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, ok_fn = function() { - this.update_from_form(); - hide_modal(); - $(window).unbind("keypress.check_enter_esc"); + self.update_from_form(); + Galaxy.modal.hide(); + $(window).unbind("keypress.check_enter_esc"); }, check_enter_esc = function(e) { if ((e.keyCode || e.which) === 27) { // Escape key @@ -246,8 +245,8 @@ this.render(); } Galaxy.modal.show({ - title: "Configure", - body: drawable.config.build_form(), + title: title || "Configure", + body: this.$el, buttons: { "Cancel": cancel_fn, "OK": ok_fn @@ -265,10 +264,10 @@ // Set value from view. var id = 'param_' + index; var value = self.$el.find( '#' + id ).val(); - if ( type === 'bool' ) { + if ( setting.get('type') === 'bool' ) { value = container.find( '#' + id ).is( ':checked' ); } - setting.set('value', value); + setting.set_value(value); } }); } diff -r c6eac0859bf917c176ec5995bff92a25841a9420 -r b2206f4ca10f8cec7c37f43f80fc24f0b93b420b static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -1,4 +1,4 @@ -define(["utils/utils", "libs/underscore", "libs/d3", "viz/visualization"], function(utils, _, d3, visualization) { +define(["utils/utils", "libs/underscore", "libs/d3", "viz/visualization", "utils/config"], function(utils, _, d3, visualization, config) { // Load needed CSS. utils.cssLoadFile("static/style/circster.css"); @@ -133,9 +133,7 @@ className: 'circster', initialize: function(options) { - this.total_gap = options.total_gap; this.genome = options.genome; - this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 10; this.label_arc_height = 50; this.scale = 1; @@ -145,7 +143,10 @@ // When tracks added to/removed from model, update view. this.model.get('drawables').on('add', this.add_track, this); this.model.get('drawables').on('remove', this.remove_track, this); - this.get_circular_tracks(); + + // When config settings change, update view. + var vis_config = this.model.get('config'); + vis_config.get('arc_dataset_height').on('change:value', this.update_track_bounds, this); }, // HACKs: using track_type for circular/chord distinction in the functions below for now. @@ -172,22 +173,22 @@ * Returns a list of circular tracks' radius bounds. */ get_tracks_bounds: function() { - var circular_tracks = this.get_circular_tracks(); - dataset_arc_height = this.dataset_arc_height, + var circular_tracks = this.get_circular_tracks(), + dataset_arc_height = this.model.get('config').get_value('arc_dataset_height'), min_dimension = Math.min(this.$el.width(), this.$el.height()), // Compute radius start based on model, will be centered // and fit entirely inside element by default. radius_start = min_dimension / 2 - - circular_tracks.length * (this.dataset_arc_height + this.track_gap) - + circular_tracks.length * (dataset_arc_height + this.track_gap) - (this.label_arc_height + this.track_gap), // Compute range of track starting radii. - tracks_start_radii = d3.range(radius_start, min_dimension / 2, this.dataset_arc_height + this.track_gap); + tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + this.track_gap); // Map from track start to bounds. var self = this; return _.map(tracks_start_radii, function(radius) { - return [radius, radius + self.dataset_arc_height]; + return [radius, radius + dataset_arc_height]; }); }, @@ -196,11 +197,11 @@ */ render: function() { var self = this, - dataset_arc_height = this.dataset_arc_height, width = self.$el.width(), height = self.$el.height(), circular_tracks = this.get_circular_tracks(), chords_tracks = this.get_chord_tracks(), + total_gap = self.model.get('config').get_value('total_gap'), tracks_bounds = this.get_tracks_bounds(), // Set up SVG element. @@ -249,7 +250,7 @@ track: track, radius_bounds: tracks_bounds[index], genome: self.genome, - total_gap: self.total_gap + total_gap: total_gap }); view.render(); @@ -265,7 +266,7 @@ track: track, radius_bounds: tracks_bounds[0], genome: self.genome, - total_gap: self.total_gap + total_gap: total_gap }); view.render(); @@ -288,7 +289,7 @@ track: new CircsterLabelTrack(), radius_bounds: track_bounds, genome: self.genome, - total_gap: self.total_gap + total_gap: total_gap }); this.label_track_view.render(); @@ -298,6 +299,8 @@ * Render a single track on the outside of the current visualization. */ add_track: function(new_track) { + var total_gap = this.model.get('config').get_value('total_gap'); + if (new_track.get('track_type') === 'DiagonalHeatmapTrack') { // Added chords track. var innermost_radius_bounds = this.circular_views[0].radius_bounds, @@ -306,7 +309,7 @@ track: new_track, radius_bounds: innermost_radius_bounds, genome: this.genome, - total_gap: this.total_gap + total_gap: total_gap }); new_view.render(); this.chords_views.push(new_view); @@ -332,7 +335,7 @@ track: new_track, radius_bounds: new_track_bounds[track_index], genome: this.genome, - total_gap: this.total_gap + total_gap: total_gap }); track_view.render(); this.circular_views.push(track_view); @@ -358,6 +361,14 @@ _.each(this.circular_views, function(track_view, i) { track_view.update_radius_bounds(new_track_bounds[i]); }); + }, + + update_track_bounds: function() { + // Recompute and update track bounds. + var new_track_bounds = this.get_tracks_bounds(); + _.each(this.circular_views, function(track_view, i) { + track_view.update_radius_bounds(new_track_bounds[i]); + }); } }); @@ -630,7 +641,7 @@ var chroms_info = this.genome.get_chroms_info(), pie_layout = d3.layout.pie().value(function(d) { return d.len; }).sort(null), init_arcs = pie_layout(chroms_info), - gap_per_chrom = this.total_gap / chroms_info.length, + gap_per_chrom = 2 * Math.PI * this.total_gap / chroms_info.length, chrom_arcs = _.map(init_arcs, function(arc, index) { // For short chroms, endAngle === startAngle. var new_endAngle = arc.endAngle - gap_per_chrom; @@ -969,22 +980,25 @@ { initialize: function () { - // configure visualization + // -- Configure visualization -- var genome = new visualization.Genome(galaxy_config.app.genome), - vis = new visualization.GenomeVisualization(galaxy_config.app.viz_config), - viz_view = new CircsterView( - { - // view pane - el : $('#center .unified-panel-body'), - - // gaps are difficult to set because it very dependent on chromosome size and organization. - total_gap : 2 * Math.PI * 0.4, - genome : genome, - model : vis, - dataset_arc_height : 25 - }); + vis = new visualization.GenomeVisualization(galaxy_config.app.viz_config); + + // Add Circster-specific config options. + vis.get('config').add([ + { key: 'arc_dataset_height', label: 'Arc Dataset Height', type: 'int', value: 25, view: 'circster' }, + { key: 'total_gap', label: 'Gap [0-1]', type: 'float', value: 0.4, view: 'circster', hidden: true } + ]); + + var viz_view = new CircsterView( + { + // view pane + el : $('#center .unified-panel-body'), + genome : genome, + model : vis + }); - // render vizualization + // Render vizualization viz_view.render(); // setup title @@ -1002,6 +1016,15 @@ } }, { + icon_class: 'gear', title: 'Settings', on_click: function() + { + var view = new config.ConfigSettingCollectionView({ + collection: vis.get('config') + }); + view.render_in_modal('Configure Visualization'); + } + }, + { icon_class: 'disk--arrow', title: 'Save', on_click: function() { // show saving dialog box Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 06 Feb '14

06 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ca4c4a24bd6a/ Changeset: ca4c4a24bd6a Branch: next-stable User: carlfeberhard Date: 2014-02-06 21:25:25 Summary: Fix css scoping in hda borders broken in 2b8e4f3 Affected #: 2 files diff -r a66e4111ba2aeca52572d203e1713153a5ee293a -r ca4c4a24bd6a853993fc171394c0d2da75fc8829 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1573,6 +1573,47 @@ .search-input .search-clear,.search-input .search-loading{position:relative;display:inline-block;float:right;margin-top:-23px;margin-right:4px;font-size:1.4em;line-height:23px;color:grey} .search-input .search-clear:hover{color:#303030} #history-refresh-button,#history-options-button{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;padding:0px} +.history-panel .dataset{border:1px solid #bfbfbf}.history-panel .dataset .vertical-spacing{margin-bottom:8px} +.history-panel .dataset .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} +.history-panel .dataset .dataset-padding{padding:6px 10px 6px 8px} +.history-panel .dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} +.history-panel .dataset .help-text{font-weight:normal;color:#555} +.history-panel .dataset .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} +.history-panel .dataset .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} +.history-panel .dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} +.history-panel .dataset .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.history-panel .dataset .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .dataset-primary-actions .icon-btn{margin-left:2px} +.history-panel .dataset .dataset-body{display:none;padding:6px 10px 6px 8px}.history-panel .dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} +.history-panel .dataset .dataset-body label{margin:0px;padding:0px;font-weight:normal} +.history-panel .dataset .dataset-body .prompt{font-weight:normal;color:#555} +.history-panel .dataset .dataset-body .prompt:after{content:':'} +.history-panel .dataset .dataset-body .dataset-summary{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} +.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} +.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} +.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.history-panel .dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} +.history-panel .dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} +.history-panel .dataset .dataset-body .dataset-actions .left{display:inline-block;float:left}.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} +.history-panel .dataset .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-actions .right{float:right}.history-panel .dataset .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} +.history-panel .dataset .dataset-body .tags-display{display:none;margin-bottom:8px}.history-panel .dataset .dataset-body .tags-display .select2-container{min-width:0px}.history-panel .dataset .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} +.history-panel .dataset .dataset-body .annotation-display{display:none;margin-bottom:8px}.history-panel .dataset .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} +.history-panel .dataset .dataset-body .annotation-display .annotation:empty{height:22px} +.history-panel .dataset .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} +.history-panel .dataset .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} +.history-panel .dataset .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-peek{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.history-panel .dataset .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} +.history-panel .dataset .dataset-body .dataset-peek pre.peek table,.history-panel .dataset .dataset-body .dataset-peek pre.peek th,.history-panel .dataset .dataset-body .dataset-peek pre.peek tr,.history-panel .dataset .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} +.history-panel .dataset .icon-btn-group{display:inline-block}.history-panel .dataset .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} +.state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .history-panel [class$="messagesmall"]{margin:0px} .history-panel .editable-text{border:solid transparent 1px} .history-panel .editable-text:hover{cursor:pointer;border:1px dotted #999999} @@ -1604,47 +1645,6 @@ .history-panel .dataset:last-child{border-width:1px 0px 1px 0px} .history-panel .empty-history-message{display:none;margin:0px 10px 0px 10px} .history-panel .tag-button{display:inline-block;height:20px;margin:2px 2px 0px 0px;border:1px solid grey;border-radius:3px 10px 10px 3px;padding:2px 4px 2px 4px;background-color:#EEE;line-height:13px}.history-panel .tag-button .tag-name{margin-right:2px} -.dataset.hda{border:1px solid #bfbfbf}.dataset.hda .vertical-spacing{margin-bottom:8px} -.dataset.hda .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} -.dataset.hda .dataset-padding{padding:6px 10px 6px 8px} -.dataset.hda [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} -.dataset.hda .help-text{font-weight:normal;color:#555} -.dataset.hda .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} -.dataset.hda .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} -.dataset.hda .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} -.dataset.hda .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.dataset.hda .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .dataset-primary-actions .icon-btn{margin-left:2px} -.dataset.hda .dataset-body{display:none;padding:6px 10px 6px 8px}.dataset.hda .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} -.dataset.hda .dataset-body label{margin:0px;padding:0px;font-weight:normal} -.dataset.hda .dataset-body .prompt{font-weight:normal;color:#555} -.dataset.hda .dataset-body .prompt:after{content:':'} -.dataset.hda .dataset-body .dataset-summary{margin-bottom:8px}.dataset.hda .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} -.dataset.hda .dataset-body .dataset-summary .dataset-datatype,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey{display:inline}.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} -.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} -.dataset.hda .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} -.dataset.hda .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.dataset.hda .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} -.dataset.hda .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} -.dataset.hda .dataset-body .dataset-actions .left{display:inline-block;float:left}.dataset.hda .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} -.dataset.hda .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} -.dataset.hda .dataset-body .dataset-actions .right{float:right}.dataset.hda .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} -.dataset.hda .dataset-body .tags-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .tags-display .select2-container{min-width:0px}.dataset.hda .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} -.dataset.hda .dataset-body .annotation-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} -.dataset.hda .dataset-body .annotation-display .annotation:empty{height:22px} -.dataset.hda .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} -.dataset.hda .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} -.dataset.hda .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} -.dataset.hda .dataset-body .dataset-peek{margin-bottom:8px}.dataset.hda .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset.hda .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} -.dataset.hda .dataset-body .dataset-peek pre.peek table,.dataset.hda .dataset-body .dataset-peek pre.peek th,.dataset.hda .dataset-body .dataset-peek pre.peek tr,.dataset.hda .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} -.dataset.hda .icon-btn-group{display:inline-block}.dataset.hda .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} -.state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .state-icon-running{-webkit-animation:spin 2s infinite linear;-moz-animation:spin 2s infinite linear;-o-animation:spin 2s infinite linear;animation:spin 2s infinite linear}@-moz-keyframes spin{0%{-moz-transform:rotate(0deg)} 100%{-moz-transform:rotate(359deg)}}@-webkit-keyframes spin{0%{-webkit-transform:rotate(0deg)} 100%{-webkit-transform:rotate(359deg)}}@-o-keyframes spin{0%{-o-transform:rotate(0deg)} 100%{-o-transform:rotate(359deg)}}@-ms-keyframes spin{0%{-ms-transform:rotate(0deg)} 100%{-ms-transform:rotate(359deg)}}@keyframes spin{0%{transform:rotate(0deg)} 100%{transform:rotate(359deg)}}.state-icon-running:before{content:"\f110"} .state-icon-upload{overflow:hidden}.state-icon-upload:before{display:inline-block;-webkit-animation:eclipse 2s infinite linear;-moz-animation:eclipse 2s infinite linear;-o-animation:eclipse 2s infinite linear;animation:eclipse 2s infinite linear;content:"\f062"}@-moz-keyframes eclipse{0%{-moz-transform:translate(0, 16px)} 100%{-moz-transform:translate(0, -16px)}}@-webkit-keyframes eclipse{0%{-webkit-transform:translate(0, 16px)} 100%{-webkit-transform:translate(0, -16px)}}@-o-keyframes eclipse{0%{-o-transform:translate(0, 16px)} 100%{-o-transform:translate(0, -16px)}}@-ms-keyframes eclipse{0%{-ms-transform:translate(0, 16px)} 100%{-ms-transform:translate(0, -16px)}}@keyframes eclipse{0%{transform:translate(0, 16px)} 100%{transform:translate(0, -16px)}} .dataset.state-ok,.dataset.state-failed_metadata{background:#aff1af}.dataset.state-ok .state-icon,.dataset.state-failed_metadata .state-icon{display:none} diff -r a66e4111ba2aeca52572d203e1713153a5ee293a -r ca4c4a24bd6a853993fc171394c0d2da75fc8829 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -98,6 +98,275 @@ } +// ---------------------------------------------------------------------------- datasets +//TODO: scope to history panels until embedded item .dataset is changed +.history-panel { + .dataset { + border: 1px solid @border-default-color; + + // body mixins + @vertical-gap: 8px; + .vertical-spacing { + margin-bottom: @vertical-gap; + } + .info-section { + border-radius: 3px; + border: 1px solid fadeout( @layout-border-color, 70% ); + //background-color: fadeout( white, 60% ); + padding: 4px; + } + @spacing-top : 6px; + @spacing-right : 10px; + @spacing-bottom : 6px; + @spacing-left : 8px; + .dataset-padding { + padding: @spacing-top @spacing-right @spacing-bottom @spacing-left; + } + + [class$=messagesmall] { + margin: @spacing-top @spacing-right ( @spacing-bottom - 4 ) @spacing-left; + font-size: 90%; + } + + .help-text { + font-weight: normal; + // font-style: italic; + // font-size: 90%; + color: #555; + } + + .dataset-selector { + float: left; + // always initially hidden and zero width + display: none; + width: 0px; + //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish + margin: 0px 0px -@spacing-bottom 0px; + padding: ( @spacing-top - 1 ) 0px 2px @spacing-left; + cursor: pointer; + //text-align: center; + vertical-align: middle; + } + + .dataset-title-bar { + cursor: pointer; + outline: none; + .dataset-padding; + + .dataset-state-icon { + } + .dataset-title { + display: inline; + font-weight: bold; + text-decoration: underline; + word-wrap: break-word; + word-break: break-all; + line-height: 16px; + } + } + + .dataset-primary-actions { + .icon-btn-group(); + float: right; + margin: @spacing-top @spacing-right 0; + .icon-btn { + margin-left: @icon-btn-margin; + } + } + + .dataset-body { + display: none; + // background-color: fadeout( white, 70% ); + .dataset-padding; + + [class$=messagesmall] { + margin: 0px 0px 8px 0px; + } + + label { + margin: 0px; + padding: 0px; + font-weight: normal; + } + .prompt { + .help-text; + } + .prompt:after { + content: ':'; + } + + .dataset-summary { + .dataset-blurb { + margin-bottom: 2px; + } + .dataset-datatype, .dataset-dbkey { + display: inline; + .value { + font-weight: bold; + } + } + .dataset-datatype .value:after { + content: ','; + .help-text; + } + .dataset-dbkey:after { + content: ' '; + display: block; + .vertical-spacing; + } + .dataset-info { + .info-section; + .value { + white-space: pre-line; + } + } + + .job-error-text { + .info-section; + overflow: auto; + white-space: pre; + } + + // handle the last vertical gap in the parent as summary is used in other states as well (w/o info) + .vertical-spacing; + } + + .dataset-actions { + .left { + .icon-btn-group(); + float: left; + .icon-btn { + margin-right: @icon-btn-margin; + } + //.icon-btn-group { + // margin-right: @icon-btn-margin; + // .icon-btn { + // margin-right: 0; + // } + //} + &:not(:empty) { + // can't use :empty on dataset-actions - will always have left & right, so + // add gap to left (more likely to have children) + .vertical-spacing; + } + } + .right { + float: right; + .icon-btn { + margin-left: @icon-btn-margin; + } + } + } + + //TODO: move these out + .tags-display { + display: none; + .vertical-spacing; + .select2-container { + min-width: 0px; + .select2-choices { + border-radius: 3px; + } + } + } + .annotation-display { + display: none; + .vertical-spacing; + .annotation { + .info-section; + white-space: pre-line; + } + .annotation:empty { + height: @icon-btn-size; + } + // fake placeholder for editable text annotation + .annotation:empty:after { + position: relative; + top: -4px; + font-size: 10px; + font-style: italic; + color: grey; + content : 'Click here to edit annotation'; + } + textarea { + margin: 0px 0px 2px 0px; + display: block; + border-radius: 3px; + width: 100%; + } + } + + .dataset-display-applications { + .display-application:last-child { + .vertical-spacing; + } + } + + .dataset-peek { + .vertical-spacing; + pre.peek { + width: 100%; + margin: 0px; + border-radius: 3px; + background: white; + color: black; + font-size: 10px; + overflow: auto; + th { + color: white; + background: @panel-primary-heading-bg; + } + table, th, tr, td { + font-family: @font-family-monospace; + font-size: 10px; + } + } + } + } + + .icon-btn-group { + display: inline-block; + .icon-btn:not(:last-child) { + margin: 0px; + border-radius: 0px; + border-right: none; + } + .icon-btn:first-child { + margin-right: 0px; + border-top-left-radius: 3px; + border-bottom-left-radius: 3px; + } + .icon-btn:last-child { + margin-left: 0px; + border-radius: 0px 3px 3px 0px; + } + } + + } + + .dataset .state-icon { + .fa-icon; + display: inline-block; + vertical-align: middle; + width: 16px; + height: 16px; + line-height: 16px; + text-align: center; + font-size: 16px; + } +} + +.state-icon-error { + background-color: white; + border-radius: 8px; + &:before { + font-size: 20px; + line-height: 16px; + color: red; + content: @fa-var-times-circle; + } +} + // ---------------------------------------------------------------------------- history .history-panel { @@ -268,272 +537,6 @@ } } -// ---------------------------------------------------------------------------- datasets -.dataset.hda { - border: 1px solid @border-default-color; - - // body mixins - @vertical-gap: 8px; - .vertical-spacing { - margin-bottom: @vertical-gap; - } - .info-section { - border-radius: 3px; - border: 1px solid fadeout( @layout-border-color, 70% ); - //background-color: fadeout( white, 60% ); - padding: 4px; - } - @spacing-top : 6px; - @spacing-right : 10px; - @spacing-bottom : 6px; - @spacing-left : 8px; - .dataset-padding { - padding: @spacing-top @spacing-right @spacing-bottom @spacing-left; - } - - [class$=messagesmall] { - margin: @spacing-top @spacing-right ( @spacing-bottom - 4 ) @spacing-left; - font-size: 90%; - } - - .help-text { - font-weight: normal; - // font-style: italic; - // font-size: 90%; - color: #555; - } - - .dataset-selector { - float: left; - // always initially hidden and zero width - display: none; - width: 0px; - //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish - margin: 0px 0px -@spacing-bottom 0px; - padding: ( @spacing-top - 1 ) 0px 2px @spacing-left; - cursor: pointer; - //text-align: center; - vertical-align: middle; - } - - .dataset-title-bar { - cursor: pointer; - outline: none; - .dataset-padding; - - .dataset-state-icon { - } - .dataset-title { - display: inline; - font-weight: bold; - text-decoration: underline; - word-wrap: break-word; - word-break: break-all; - line-height: 16px; - } - } - - .dataset-primary-actions { - .icon-btn-group(); - float: right; - margin: @spacing-top @spacing-right 0; - .icon-btn { - margin-left: @icon-btn-margin; - } - } - - .dataset-body { - display: none; - // background-color: fadeout( white, 70% ); - .dataset-padding; - - [class$=messagesmall] { - margin: 0px 0px 8px 0px; - } - - label { - margin: 0px; - padding: 0px; - font-weight: normal; - } - .prompt { - .help-text; - } - .prompt:after { - content: ':'; - } - - .dataset-summary { - .dataset-blurb { - margin-bottom: 2px; - } - .dataset-datatype, .dataset-dbkey { - display: inline; - .value { - font-weight: bold; - } - } - .dataset-datatype .value:after { - content: ','; - .help-text; - } - .dataset-dbkey:after { - content: ' '; - display: block; - .vertical-spacing; - } - .dataset-info { - .info-section; - .value { - white-space: pre-line; - } - } - - .job-error-text { - .info-section; - overflow: auto; - white-space: pre; - } - - // handle the last vertical gap in the parent as summary is used in other states as well (w/o info) - .vertical-spacing; - } - - .dataset-actions { - .left { - .icon-btn-group(); - float: left; - .icon-btn { - margin-right: @icon-btn-margin; - } - //.icon-btn-group { - // margin-right: @icon-btn-margin; - // .icon-btn { - // margin-right: 0; - // } - //} - &:not(:empty) { - // can't use :empty on dataset-actions - will always have left & right, so - // add gap to left (more likely to have children) - .vertical-spacing; - } - } - .right { - float: right; - .icon-btn { - margin-left: @icon-btn-margin; - } - } - } - - //TODO: move these out - .tags-display { - display: none; - .vertical-spacing; - .select2-container { - min-width: 0px; - .select2-choices { - border-radius: 3px; - } - } - } - .annotation-display { - display: none; - .vertical-spacing; - .annotation { - .info-section; - white-space: pre-line; - } - .annotation:empty { - height: @icon-btn-size; - } - // fake placeholder for editable text annotation - .annotation:empty:after { - position: relative; - top: -4px; - font-size: 10px; - font-style: italic; - color: grey; - content : 'Click here to edit annotation'; - } - textarea { - margin: 0px 0px 2px 0px; - display: block; - border-radius: 3px; - width: 100%; - } - } - - .dataset-display-applications { - .display-application:last-child { - .vertical-spacing; - } - } - - .dataset-peek { - .vertical-spacing; - pre.peek { - width: 100%; - margin: 0px; - border-radius: 3px; - background: white; - color: black; - font-size: 10px; - overflow: auto; - th { - color: white; - background: @panel-primary-heading-bg; - } - table, th, tr, td { - font-family: @font-family-monospace; - font-size: 10px; - } - } - } - } - - .icon-btn-group { - display: inline-block; - .icon-btn:not(:last-child) { - margin: 0px; - border-radius: 0px; - border-right: none; - } - .icon-btn:first-child { - margin-right: 0px; - border-top-left-radius: 3px; - border-bottom-left-radius: 3px; - } - .icon-btn:last-child { - margin-left: 0px; - border-radius: 0px 3px 3px 0px; - } - } - -} - -.dataset.hda .state-icon { - .fa-icon; - display: inline-block; - vertical-align: middle; - width: 16px; - height: 16px; - line-height: 16px; - text-align: center; - font-size: 16px; -} - -.state-icon-error { - background-color: white; - border-radius: 8px; - &:before { - font-size: 20px; - line-height: 16px; - color: red; - content: @fa-var-times-circle; - } -} - .state-icon-running { //TODO: couldn't find a way to do this with fa/spinning.less as mixin -webkit-animation: spin 2s infinite linear; https://bitbucket.org/galaxy/galaxy-central/commits/c6eac0859bf9/ Changeset: c6eac0859bf9 User: carlfeberhard Date: 2014-02-06 21:25:58 Summary: merge Affected #: 2 files diff -r 3db994bbb5794de782a824b5ea8b2220b99e97ec -r c6eac0859bf917c176ec5995bff92a25841a9420 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1574,6 +1574,47 @@ .search-input .search-clear,.search-input .search-loading{position:relative;display:inline-block;float:right;margin-top:-23px;margin-right:4px;font-size:1.4em;line-height:23px;color:grey} .search-input .search-clear:hover{color:#303030} #history-refresh-button,#history-options-button{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;padding:0px} +.history-panel .dataset{border:1px solid #bfbfbf}.history-panel .dataset .vertical-spacing{margin-bottom:8px} +.history-panel .dataset .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} +.history-panel .dataset .dataset-padding{padding:6px 10px 6px 8px} +.history-panel .dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} +.history-panel .dataset .help-text{font-weight:normal;color:#555} +.history-panel .dataset .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} +.history-panel .dataset .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} +.history-panel .dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} +.history-panel .dataset .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.history-panel .dataset .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .dataset-primary-actions .icon-btn{margin-left:2px} +.history-panel .dataset .dataset-body{display:none;padding:6px 10px 6px 8px}.history-panel .dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} +.history-panel .dataset .dataset-body label{margin:0px;padding:0px;font-weight:normal} +.history-panel .dataset .dataset-body .prompt{font-weight:normal;color:#555} +.history-panel .dataset .dataset-body .prompt:after{content:':'} +.history-panel .dataset .dataset-body .dataset-summary{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} +.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} +.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} +.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.history-panel .dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} +.history-panel .dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} +.history-panel .dataset .dataset-body .dataset-actions .left{display:inline-block;float:left}.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} +.history-panel .dataset .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-actions .right{float:right}.history-panel .dataset .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} +.history-panel .dataset .dataset-body .tags-display{display:none;margin-bottom:8px}.history-panel .dataset .dataset-body .tags-display .select2-container{min-width:0px}.history-panel .dataset .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} +.history-panel .dataset .dataset-body .annotation-display{display:none;margin-bottom:8px}.history-panel .dataset .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} +.history-panel .dataset .dataset-body .annotation-display .annotation:empty{height:22px} +.history-panel .dataset .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} +.history-panel .dataset .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} +.history-panel .dataset .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} +.history-panel .dataset .dataset-body .dataset-peek{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.history-panel .dataset .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} +.history-panel .dataset .dataset-body .dataset-peek pre.peek table,.history-panel .dataset .dataset-body .dataset-peek pre.peek th,.history-panel .dataset .dataset-body .dataset-peek pre.peek tr,.history-panel .dataset .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} +.history-panel .dataset .icon-btn-group{display:inline-block}.history-panel .dataset .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} +.history-panel .dataset .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} +.history-panel .dataset .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} +.history-panel .dataset .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} +.state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .history-panel [class$="messagesmall"]{margin:0px} .history-panel .editable-text{border:solid transparent 1px} .history-panel .editable-text:hover{cursor:pointer;border:1px dotted #999999} @@ -1605,47 +1646,6 @@ .history-panel .dataset:last-child{border-width:1px 0px 1px 0px} .history-panel .empty-history-message{display:none;margin:0px 10px 0px 10px} .history-panel .tag-button{display:inline-block;height:20px;margin:2px 2px 0px 0px;border:1px solid grey;border-radius:3px 10px 10px 3px;padding:2px 4px 2px 4px;background-color:#EEE;line-height:13px}.history-panel .tag-button .tag-name{margin-right:2px} -.dataset.hda{border:1px solid #bfbfbf}.dataset.hda .vertical-spacing{margin-bottom:8px} -.dataset.hda .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} -.dataset.hda .dataset-padding{padding:6px 10px 6px 8px} -.dataset.hda [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} -.dataset.hda .help-text{font-weight:normal;color:#555} -.dataset.hda .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} -.dataset.hda .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} -.dataset.hda .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} -.dataset.hda .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.dataset.hda .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .dataset-primary-actions .icon-btn{margin-left:2px} -.dataset.hda .dataset-body{display:none;padding:6px 10px 6px 8px}.dataset.hda .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} -.dataset.hda .dataset-body label{margin:0px;padding:0px;font-weight:normal} -.dataset.hda .dataset-body .prompt{font-weight:normal;color:#555} -.dataset.hda .dataset-body .prompt:after{content:':'} -.dataset.hda .dataset-body .dataset-summary{margin-bottom:8px}.dataset.hda .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} -.dataset.hda .dataset-body .dataset-summary .dataset-datatype,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey{display:inline}.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value,.dataset.hda .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} -.dataset.hda .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} -.dataset.hda .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} -.dataset.hda .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.dataset.hda .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} -.dataset.hda .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} -.dataset.hda .dataset-body .dataset-actions .left{display:inline-block;float:left}.dataset.hda .dataset-body .dataset-actions .left .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} -.dataset.hda .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} -.dataset.hda .dataset-body .dataset-actions .right{float:right}.dataset.hda .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} -.dataset.hda .dataset-body .tags-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .tags-display .select2-container{min-width:0px}.dataset.hda .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} -.dataset.hda .dataset-body .annotation-display{display:none;margin-bottom:8px}.dataset.hda .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} -.dataset.hda .dataset-body .annotation-display .annotation:empty{height:22px} -.dataset.hda .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} -.dataset.hda .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} -.dataset.hda .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} -.dataset.hda .dataset-body .dataset-peek{margin-bottom:8px}.dataset.hda .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset.hda .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} -.dataset.hda .dataset-body .dataset-peek pre.peek table,.dataset.hda .dataset-body .dataset-peek pre.peek th,.dataset.hda .dataset-body .dataset-peek pre.peek tr,.dataset.hda .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} -.dataset.hda .icon-btn-group{display:inline-block}.dataset.hda .icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} -.dataset.hda .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} -.dataset.hda .icon-btn-group .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} -.dataset.hda .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} -.state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .state-icon-running{-webkit-animation:spin 2s infinite linear;-moz-animation:spin 2s infinite linear;-o-animation:spin 2s infinite linear;animation:spin 2s infinite linear}@-moz-keyframes spin{0%{-moz-transform:rotate(0deg)} 100%{-moz-transform:rotate(359deg)}}@-webkit-keyframes spin{0%{-webkit-transform:rotate(0deg)} 100%{-webkit-transform:rotate(359deg)}}@-o-keyframes spin{0%{-o-transform:rotate(0deg)} 100%{-o-transform:rotate(359deg)}}@-ms-keyframes spin{0%{-ms-transform:rotate(0deg)} 100%{-ms-transform:rotate(359deg)}}@keyframes spin{0%{transform:rotate(0deg)} 100%{transform:rotate(359deg)}}.state-icon-running:before{content:"\f110"} .state-icon-upload{overflow:hidden}.state-icon-upload:before{display:inline-block;-webkit-animation:eclipse 2s infinite linear;-moz-animation:eclipse 2s infinite linear;-o-animation:eclipse 2s infinite linear;animation:eclipse 2s infinite linear;content:"\f062"}@-moz-keyframes eclipse{0%{-moz-transform:translate(0, 16px)} 100%{-moz-transform:translate(0, -16px)}}@-webkit-keyframes eclipse{0%{-webkit-transform:translate(0, 16px)} 100%{-webkit-transform:translate(0, -16px)}}@-o-keyframes eclipse{0%{-o-transform:translate(0, 16px)} 100%{-o-transform:translate(0, -16px)}}@-ms-keyframes eclipse{0%{-ms-transform:translate(0, 16px)} 100%{-ms-transform:translate(0, -16px)}}@keyframes eclipse{0%{transform:translate(0, 16px)} 100%{transform:translate(0, -16px)}} .dataset.state-ok,.dataset.state-failed_metadata{background:#aff1af}.dataset.state-ok .state-icon,.dataset.state-failed_metadata .state-icon{display:none} diff -r 3db994bbb5794de782a824b5ea8b2220b99e97ec -r c6eac0859bf917c176ec5995bff92a25841a9420 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -98,6 +98,275 @@ } +// ---------------------------------------------------------------------------- datasets +//TODO: scope to history panels until embedded item .dataset is changed +.history-panel { + .dataset { + border: 1px solid @border-default-color; + + // body mixins + @vertical-gap: 8px; + .vertical-spacing { + margin-bottom: @vertical-gap; + } + .info-section { + border-radius: 3px; + border: 1px solid fadeout( @layout-border-color, 70% ); + //background-color: fadeout( white, 60% ); + padding: 4px; + } + @spacing-top : 6px; + @spacing-right : 10px; + @spacing-bottom : 6px; + @spacing-left : 8px; + .dataset-padding { + padding: @spacing-top @spacing-right @spacing-bottom @spacing-left; + } + + [class$=messagesmall] { + margin: @spacing-top @spacing-right ( @spacing-bottom - 4 ) @spacing-left; + font-size: 90%; + } + + .help-text { + font-weight: normal; + // font-style: italic; + // font-size: 90%; + color: #555; + } + + .dataset-selector { + float: left; + // always initially hidden and zero width + display: none; + width: 0px; + //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish + margin: 0px 0px -@spacing-bottom 0px; + padding: ( @spacing-top - 1 ) 0px 2px @spacing-left; + cursor: pointer; + //text-align: center; + vertical-align: middle; + } + + .dataset-title-bar { + cursor: pointer; + outline: none; + .dataset-padding; + + .dataset-state-icon { + } + .dataset-title { + display: inline; + font-weight: bold; + text-decoration: underline; + word-wrap: break-word; + word-break: break-all; + line-height: 16px; + } + } + + .dataset-primary-actions { + .icon-btn-group(); + float: right; + margin: @spacing-top @spacing-right 0; + .icon-btn { + margin-left: @icon-btn-margin; + } + } + + .dataset-body { + display: none; + // background-color: fadeout( white, 70% ); + .dataset-padding; + + [class$=messagesmall] { + margin: 0px 0px 8px 0px; + } + + label { + margin: 0px; + padding: 0px; + font-weight: normal; + } + .prompt { + .help-text; + } + .prompt:after { + content: ':'; + } + + .dataset-summary { + .dataset-blurb { + margin-bottom: 2px; + } + .dataset-datatype, .dataset-dbkey { + display: inline; + .value { + font-weight: bold; + } + } + .dataset-datatype .value:after { + content: ','; + .help-text; + } + .dataset-dbkey:after { + content: ' '; + display: block; + .vertical-spacing; + } + .dataset-info { + .info-section; + .value { + white-space: pre-line; + } + } + + .job-error-text { + .info-section; + overflow: auto; + white-space: pre; + } + + // handle the last vertical gap in the parent as summary is used in other states as well (w/o info) + .vertical-spacing; + } + + .dataset-actions { + .left { + .icon-btn-group(); + float: left; + .icon-btn { + margin-right: @icon-btn-margin; + } + //.icon-btn-group { + // margin-right: @icon-btn-margin; + // .icon-btn { + // margin-right: 0; + // } + //} + &:not(:empty) { + // can't use :empty on dataset-actions - will always have left & right, so + // add gap to left (more likely to have children) + .vertical-spacing; + } + } + .right { + float: right; + .icon-btn { + margin-left: @icon-btn-margin; + } + } + } + + //TODO: move these out + .tags-display { + display: none; + .vertical-spacing; + .select2-container { + min-width: 0px; + .select2-choices { + border-radius: 3px; + } + } + } + .annotation-display { + display: none; + .vertical-spacing; + .annotation { + .info-section; + white-space: pre-line; + } + .annotation:empty { + height: @icon-btn-size; + } + // fake placeholder for editable text annotation + .annotation:empty:after { + position: relative; + top: -4px; + font-size: 10px; + font-style: italic; + color: grey; + content : 'Click here to edit annotation'; + } + textarea { + margin: 0px 0px 2px 0px; + display: block; + border-radius: 3px; + width: 100%; + } + } + + .dataset-display-applications { + .display-application:last-child { + .vertical-spacing; + } + } + + .dataset-peek { + .vertical-spacing; + pre.peek { + width: 100%; + margin: 0px; + border-radius: 3px; + background: white; + color: black; + font-size: 10px; + overflow: auto; + th { + color: white; + background: @panel-primary-heading-bg; + } + table, th, tr, td { + font-family: @font-family-monospace; + font-size: 10px; + } + } + } + } + + .icon-btn-group { + display: inline-block; + .icon-btn:not(:last-child) { + margin: 0px; + border-radius: 0px; + border-right: none; + } + .icon-btn:first-child { + margin-right: 0px; + border-top-left-radius: 3px; + border-bottom-left-radius: 3px; + } + .icon-btn:last-child { + margin-left: 0px; + border-radius: 0px 3px 3px 0px; + } + } + + } + + .dataset .state-icon { + .fa-icon; + display: inline-block; + vertical-align: middle; + width: 16px; + height: 16px; + line-height: 16px; + text-align: center; + font-size: 16px; + } +} + +.state-icon-error { + background-color: white; + border-radius: 8px; + &:before { + font-size: 20px; + line-height: 16px; + color: red; + content: @fa-var-times-circle; + } +} + // ---------------------------------------------------------------------------- history .history-panel { @@ -268,272 +537,6 @@ } } -// ---------------------------------------------------------------------------- datasets -.dataset.hda { - border: 1px solid @border-default-color; - - // body mixins - @vertical-gap: 8px; - .vertical-spacing { - margin-bottom: @vertical-gap; - } - .info-section { - border-radius: 3px; - border: 1px solid fadeout( @layout-border-color, 70% ); - //background-color: fadeout( white, 60% ); - padding: 4px; - } - @spacing-top : 6px; - @spacing-right : 10px; - @spacing-bottom : 6px; - @spacing-left : 8px; - .dataset-padding { - padding: @spacing-top @spacing-right @spacing-bottom @spacing-left; - } - - [class$=messagesmall] { - margin: @spacing-top @spacing-right ( @spacing-bottom - 4 ) @spacing-left; - font-size: 90%; - } - - .help-text { - font-weight: normal; - // font-style: italic; - // font-size: 90%; - color: #555; - } - - .dataset-selector { - float: left; - // always initially hidden and zero width - display: none; - width: 0px; - //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish - margin: 0px 0px -@spacing-bottom 0px; - padding: ( @spacing-top - 1 ) 0px 2px @spacing-left; - cursor: pointer; - //text-align: center; - vertical-align: middle; - } - - .dataset-title-bar { - cursor: pointer; - outline: none; - .dataset-padding; - - .dataset-state-icon { - } - .dataset-title { - display: inline; - font-weight: bold; - text-decoration: underline; - word-wrap: break-word; - word-break: break-all; - line-height: 16px; - } - } - - .dataset-primary-actions { - .icon-btn-group(); - float: right; - margin: @spacing-top @spacing-right 0; - .icon-btn { - margin-left: @icon-btn-margin; - } - } - - .dataset-body { - display: none; - // background-color: fadeout( white, 70% ); - .dataset-padding; - - [class$=messagesmall] { - margin: 0px 0px 8px 0px; - } - - label { - margin: 0px; - padding: 0px; - font-weight: normal; - } - .prompt { - .help-text; - } - .prompt:after { - content: ':'; - } - - .dataset-summary { - .dataset-blurb { - margin-bottom: 2px; - } - .dataset-datatype, .dataset-dbkey { - display: inline; - .value { - font-weight: bold; - } - } - .dataset-datatype .value:after { - content: ','; - .help-text; - } - .dataset-dbkey:after { - content: ' '; - display: block; - .vertical-spacing; - } - .dataset-info { - .info-section; - .value { - white-space: pre-line; - } - } - - .job-error-text { - .info-section; - overflow: auto; - white-space: pre; - } - - // handle the last vertical gap in the parent as summary is used in other states as well (w/o info) - .vertical-spacing; - } - - .dataset-actions { - .left { - .icon-btn-group(); - float: left; - .icon-btn { - margin-right: @icon-btn-margin; - } - //.icon-btn-group { - // margin-right: @icon-btn-margin; - // .icon-btn { - // margin-right: 0; - // } - //} - &:not(:empty) { - // can't use :empty on dataset-actions - will always have left & right, so - // add gap to left (more likely to have children) - .vertical-spacing; - } - } - .right { - float: right; - .icon-btn { - margin-left: @icon-btn-margin; - } - } - } - - //TODO: move these out - .tags-display { - display: none; - .vertical-spacing; - .select2-container { - min-width: 0px; - .select2-choices { - border-radius: 3px; - } - } - } - .annotation-display { - display: none; - .vertical-spacing; - .annotation { - .info-section; - white-space: pre-line; - } - .annotation:empty { - height: @icon-btn-size; - } - // fake placeholder for editable text annotation - .annotation:empty:after { - position: relative; - top: -4px; - font-size: 10px; - font-style: italic; - color: grey; - content : 'Click here to edit annotation'; - } - textarea { - margin: 0px 0px 2px 0px; - display: block; - border-radius: 3px; - width: 100%; - } - } - - .dataset-display-applications { - .display-application:last-child { - .vertical-spacing; - } - } - - .dataset-peek { - .vertical-spacing; - pre.peek { - width: 100%; - margin: 0px; - border-radius: 3px; - background: white; - color: black; - font-size: 10px; - overflow: auto; - th { - color: white; - background: @panel-primary-heading-bg; - } - table, th, tr, td { - font-family: @font-family-monospace; - font-size: 10px; - } - } - } - } - - .icon-btn-group { - display: inline-block; - .icon-btn:not(:last-child) { - margin: 0px; - border-radius: 0px; - border-right: none; - } - .icon-btn:first-child { - margin-right: 0px; - border-top-left-radius: 3px; - border-bottom-left-radius: 3px; - } - .icon-btn:last-child { - margin-left: 0px; - border-radius: 0px 3px 3px 0px; - } - } - -} - -.dataset.hda .state-icon { - .fa-icon; - display: inline-block; - vertical-align: middle; - width: 16px; - height: 16px; - line-height: 16px; - text-align: center; - font-size: 16px; -} - -.state-icon-error { - background-color: white; - border-radius: 8px; - &:before { - font-size: 20px; - line-height: 16px; - color: red; - content: @fa-var-times-circle; - } -} - .state-icon-running { //TODO: couldn't find a way to do this with fa/spinning.less as mixin -webkit-animation: spin 2s infinite linear; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit 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