galaxy-commits February 2014

galaxy-commits@lists.galaxyproject.org

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192 discussions

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/aefe5cf99f92/ Changeset: aefe5cf99f92 Branch: next-stable User: abretaud Date: 2014-02-07 11:51:41 Summary: Fix crash when recovering jobs of a removed tool Affected #: 1 file diff -r deea87095946ea32d28491b44a120bbc94683150 -r aefe5cf99f92eaa3a401f3f7a9edf9dce4027ed1 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -107,7 +107,7 @@ if job.tool_id not in self.app.toolbox.tools_by_id: log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) ) JobWrapper( job, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator.' ) - if job.job_runner_name is not None and job.job_runner_external_id is None: + elif job.job_runner_name is not None and job.job_runner_external_id is None: # This could happen during certain revisions of Galaxy where a runner URL was persisted before the job was dispatched to a runner. log.debug( "(%s) Job runner assigned but no external ID recorded, adding to the job handler queue" % job.id ) job.job_runner_name = None https://bitbucket.org/galaxy/galaxy-central/commits/5e2a4255cf09/ Changeset: 5e2a4255cf09 User: natefoo Date: 2014-02-07 15:27:14 Summary: merge. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: abretaud: Fix crash when recovering jobs of a removed tool
by commits-noreply＠bitbucket.org 07 Feb '14

07 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f6f6529b8ca1/ Changeset: f6f6529b8ca1 User: abretaud Date: 2014-02-07 11:51:41 Summary: Fix crash when recovering jobs of a removed tool Affected #: 1 file diff -r 086e594d372cc58a823f061c3a008a60c0c33472 -r f6f6529b8ca14267bdd3c4ab1fcd2343dffc08dd lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -107,7 +107,7 @@ if job.tool_id not in self.app.toolbox.tools_by_id: log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) ) JobWrapper( job, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator.' ) - if job.job_runner_name is not None and job.job_runner_external_id is None: + elif job.job_runner_name is not None and job.job_runner_external_id is None: # This could happen during certain revisions of Galaxy where a runner URL was persisted before the job was dispatched to a runner. log.debug( "(%s) Job runner assigned but no external ID recorded, adding to the job handler queue" % job.id ) job.job_runner_name = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 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 07 Feb '14

07 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 07 Feb '14

07 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 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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 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_.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 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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 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:"'+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.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 07 Feb '14

07 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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galaxy-commits February 2014