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commit/galaxy-central: jmchilton: Modify Docker set_user option to allow setting a remote user.
by commits-noreply＠bitbucket.org 17 Nov '14

17 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0134276d67f7/ Changeset: 0134276d67f7 User: jmchilton Date: 2014-11-17 17:16:12+00:00 Summary: Modify Docker set_user option to allow setting a remote user. Now is disabled by setting this to the empty string instead of false. Add flexibility allows working around the fact that it is not evaluated properly for Pulsar by setting this to be the remote pulsar user :(. Longer term the default option should be the remote user on the worker node instead of the Galaxy user. I don't believe this feature has been in stable so I am not preserving backward compatiblity. Affected #: 3 files diff -r a1aa1dbc8cb6249b4ca39f0e4cda500abcafae82 -r 0134276d67f7a70d5e7afb7e876362c557044f86 config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -199,7 +199,11 @@ will be removed automatically after the program is complete. --> -  +  + <!-- Following can be used to connect to docke server in different diff -r a1aa1dbc8cb6249b4ca39f0e4cda500abcafae82 -r 0134276d67f7a70d5e7afb7e876362c557044f86 lib/galaxy/tools/deps/containers.py --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -244,7 +244,7 @@ working_directory=working_directory, net=prop("net", "none"), # By default, docker instance has networking disabled auto_rm=asbool(prop("auto_rm", docker_util.DEFAULT_AUTO_REMOVE)), - set_user=asbool(prop("set_user", docker_util.DEFAULT_SET_USER)), + set_user=prop("set_user", docker_util.DEFAULT_SET_USER), **docker_host_props ) return "%s\n%s" % (cache_command, run_command) diff -r a1aa1dbc8cb6249b4ca39f0e4cda500abcafae82 -r 0134276d67f7a70d5e7afb7e876362c557044f86 lib/galaxy/tools/deps/docker_util.py --- a/lib/galaxy/tools/deps/docker_util.py +++ b/lib/galaxy/tools/deps/docker_util.py @@ -10,7 +10,7 @@ DEFAULT_MEMORY = None DEFAULT_VOLUMES_FROM = None DEFAULT_AUTO_REMOVE = True -DEFAULT_SET_USER = True +DEFAULT_SET_USER = "$UID" class DockerVolume(object): @@ -149,7 +149,10 @@ if auto_rm: command_parts.append("--rm") if set_user: - command_parts.extend(["-u", str(os.geteuid())]) + user = set_user + if set_user == DEFAULT_SET_USER: + user = str(os.geteuid()) + command_parts.extend(["-u", user]) full_image = image if tag: full_image = "%s:%s" % (full_image, tag) 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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[galaxyproject/usegalaxy-playbook] 665492: Allocate 16 GB for an additional set of tools (mos...
by GitHub 17 Nov '14

17 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 665492ca686525339ee573eb379387c7ad649199 https://github.com/galaxyproject/usegalaxy-playbook/commit/665492ca68652533… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-11-17 (Mon, 17 Nov 2014) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Allocate 16 GB for an additional set of tools (mostly GATK).

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commit/galaxy-central: jmchilton: Merge stable.
by commits-noreply＠bitbucket.org 17 Nov '14

17 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a1aa1dbc8cb6/ Changeset: a1aa1dbc8cb6 User: jmchilton Date: 2014-11-17 15:40:51+00:00 Summary: Merge stable. Affected #: 7 files diff -r a4f509eb288327415a231c83a79a7aa324d5fe4f -r a1aa1dbc8cb6249b4ca39f0e4cda500abcafae82 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -a1dca14d5b1afbf2b5bde192e3e6b6763836eff8 latest_2014.10.06 +011c8b2118be778eaf1ba952730ff876d6447ba9 latest_2014.10.06 diff -r a4f509eb288327415a231c83a79a7aa324d5fe4f -r a1aa1dbc8cb6249b4ca39f0e4cda500abcafae82 client/galaxy/scripts/mvc/citation/citation-view.js --- a/client/galaxy/scripts/mvc/citation/citation-view.js +++ b/client/galaxy/scripts/mvc/citation/citation-view.js @@ -58,11 +58,11 @@ var doiUrl = ""; if( fields.doi ) { doiUrl = 'http://dx.doi.org/' + fields.doi; - ref += '[<a href="' + doiUrl + '">doi:' + fields.doi + "</a>]"; + ref += '[<a href="' + doiUrl + '" target="_blank">doi:' + fields.doi + "</a>]"; } var url = fields.url || doiUrl; if( url ) { - ref += '[<a href="' + url + '">Link</a>]'; + ref += '[<a href="' + url + '" target="_blank">Link</a>]'; } return ref; }, @@ -185,4 +185,4 @@ CitationListView : CitationListView }; -}); \ No newline at end of file +}); diff -r a4f509eb288327415a231c83a79a7aa324d5fe4f -r a1aa1dbc8cb6249b4ca39f0e4cda500abcafae82 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2615,14 +2615,20 @@ history = None value = input.test_param.get_initial_value( trans, context, history=history ) current_case = input.get_current_case( value, trans ) - if current_case != old_current_case: + case_changed = current_case != old_current_case + if case_changed: # Current case has changed, throw away old state group_state = state[input.name] = {} # TODO: we should try to preserve values if we can self.fill_in_new_state( trans, input.cases[current_case].inputs, group_state, context ) group_errors = dict() group_old_errors = dict() - else: + + # If we didn't just change the current case and are coming from HTML - the values + # in incoming represent the old values and should not be replaced. If being updated + # from the API (json) instead of HTML - form values below the current case + # may also be supplied and incoming should be preferred to case defaults. + if (not case_changed) or (source != "html"): # Current case has not changed, update children group_errors = self.update_state( trans, input.cases[current_case].inputs, diff -r a4f509eb288327415a231c83a79a7aa324d5fe4f -r a1aa1dbc8cb6249b4ca39f0e4cda500abcafae82 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -727,7 +727,7 @@ old_errors = state.inputs.pop( "__errors__", {} ) # Update the state step_errors = tool.update_state( trans, tool.inputs, state.inputs, step_updates, - update_only=True, old_errors=old_errors ) + update_only=True, old_errors=old_errors, source="json" ) return state, step_errors def execute( self, trans, progress, invocation, step ): diff -r a4f509eb288327415a231c83a79a7aa324d5fe4f -r a1aa1dbc8cb6249b4ca39f0e4cda500abcafae82 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -117,7 +117,32 @@ param_dict[param_dict['param']] = param_dict['value'] del param_dict[ 'param' ] del param_dict[ 'value' ] - return param_dict + # Inputs can be nested dict, but Galaxy tool code wants nesting of keys (e.g. + # cond1|moo=4 instead of cond1: {moo: 4} ). + new_params = _flatten_step_params( param_dict ) + return new_params + + +def _flatten_step_params( param_dict, prefix="" ): + # TODO: Temporary work around until tool code can process nested data + # structures. This should really happen in there so the tools API gets + # this functionality for free and so that repeats can be handled + # properly. Also the tool code walks the tool inputs so it nows what is + # a complex value object versus something that maps to child parameters + # better than the hack or searching for src and id here. + new_params = {} + keys = param_dict.keys()[:] + for key in keys: + if prefix: + effective_key = "%s|%s" % ( prefix, key ) + else: + effective_key = key + value = param_dict[key] + if isinstance(value, dict) and not ('src' in value and 'id' in value): + new_params.update(_flatten_step_params( value, effective_key) ) + else: + new_params[effective_key] = value + return new_params def build_workflow_run_config( trans, workflow, payload ): diff -r a4f509eb288327415a231c83a79a7aa324d5fe4f -r a1aa1dbc8cb6249b4ca39f0e4cda500abcafae82 static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -58,11 +58,11 @@ var doiUrl = ""; if( fields.doi ) { doiUrl = 'http://dx.doi.org/' + fields.doi; - ref += '[<a href="' + doiUrl + '">doi:' + fields.doi + "</a>]"; + ref += '[<a href="' + doiUrl + '" target="_blank">doi:' + fields.doi + "</a>]"; } var url = fields.url || doiUrl; if( url ) { - ref += '[<a href="' + url + '">Link</a>]'; + ref += '[<a href="' + url + '" target="_blank">Link</a>]'; } return ref; }, @@ -185,4 +185,4 @@ CitationListView : CitationListView }; -}); \ No newline at end of file +}); diff -r a4f509eb288327415a231c83a79a7aa324d5fe4f -r a1aa1dbc8cb6249b4ca39f0e4cda500abcafae82 static/scripts/packed/mvc/citation/citation-view.js --- a/static/scripts/packed/mvc/citation/citation-view.js +++ b/static/scripts/packed/mvc/citation/citation-view.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var k=this.model;var i=k.entryType();var l=k.fields();var g="";var o=this._asSentence((l.author?l.author:"")+(l.year?(" ("+l.year+")"):""))+" ";var n=l.title||"";var h=l.pages?("pp. "+l.pages):"";var p=l.address;if(i=="article"){var j=(l.volume?l.volume:"")+(l.number?(" ("+l.number+")"):"")+(h?", "+h:"");g=o+this._asSentence(n)+(l.journal?("In <em>"+l.journal+", "):"")+this._asSentence(j)+this._asSentence(l.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=o+this._asSentence(n)+(l.booktitle?("In <em>"+l.booktitle+", "):"")+(h?h:"")+(p?", "+p:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=o+this._asSentence(n)+(l.howpublished?l.howpublished+". ":"")+(l.note?l.note+".":"")}else{if(i=="techreport"){g=o+this._asSentence(n)+this._asSentence(l.institution)+this._asSentence(l.number)+this._asSentence(l.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=o+" "+this._formatBookInfo(l)}else{g=o+" "+this._asSentence(n)+this._asSentence(l.howpublished)+this._asSentence(l.note)}}}}}var m="";if(l.doi){m="http://dx.doi.org/"+l.doi;g+='[<a href="'+m+'">doi:'+l.doi+"</a>]"}var f=l.url||m;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file +define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var k=this.model;var i=k.entryType();var l=k.fields();var g="";var o=this._asSentence((l.author?l.author:"")+(l.year?(" ("+l.year+")"):""))+" ";var n=l.title||"";var h=l.pages?("pp. "+l.pages):"";var p=l.address;if(i=="article"){var j=(l.volume?l.volume:"")+(l.number?(" ("+l.number+")"):"")+(h?", "+h:"");g=o+this._asSentence(n)+(l.journal?("In <em>"+l.journal+", "):"")+this._asSentence(j)+this._asSentence(l.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=o+this._asSentence(n)+(l.booktitle?("In <em>"+l.booktitle+", "):"")+(h?h:"")+(p?", "+p:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=o+this._asSentence(n)+(l.howpublished?l.howpublished+". ":"")+(l.note?l.note+".":"")}else{if(i=="techreport"){g=o+this._asSentence(n)+this._asSentence(l.institution)+this._asSentence(l.number)+this._asSentence(l.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=o+" "+this._formatBookInfo(l)}else{g=o+" "+this._asSentence(n)+this._asSentence(l.howpublished)+this._asSentence(l.note)}}}}}var m="";if(l.doi){m="http://dx.doi.org/"+l.doi;g+='[<a href="'+m+'" target="_blank">doi:'+l.doi+"</a>]"}var f=l.url||m;if(f){g+='[<a href="'+f+'" target="_blank">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file 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: ToolForm: Add switch for new tool form to configuration
by commits-noreply＠bitbucket.org 17 Nov '14

17 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a4f509eb2883/ Changeset: a4f509eb2883 User: guerler Date: 2014-11-17 15:42:56+00:00 Summary: ToolForm: Add switch for new tool form to configuration Affected #: 5 files diff -r 46087ed045d8dbb6570393d5223ba5bd0772b7e4 -r a4f509eb288327415a231c83a79a7aa324d5fe4f client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -324,7 +324,7 @@ }); // switch to classic tool form mako if the form definition is incompatible - if (this.incompatible) { + if (this.incompatible || !this.options.toolform_upgrade) { this.$el.hide(); $('#tool-form-classic').show(); return; diff -r 46087ed045d8dbb6570393d5223ba5bd0772b7e4 -r a4f509eb288327415a231c83a79a7aa324d5fe4f config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -742,6 +742,9 @@ # -- Beta features +# Use new tool form +#toolform_upgrade = False + # Enable Galaxy to communicate directly with a sequencer #enable_sequencer_communication = False diff -r 46087ed045d8dbb6570393d5223ba5bd0772b7e4 -r a4f509eb288327415a231c83a79a7aa324d5fe4f static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -324,7 +324,7 @@ }); // switch to classic tool form mako if the form definition is incompatible - if (this.incompatible) { + if (this.incompatible || !this.options.toolform_upgrade) { this.$el.hide(); $('#tool-form-classic').show(); return; diff -r 46087ed045d8dbb6570393d5223ba5bd0772b7e4 -r a4f509eb288327415a231c83a79a7aa324d5fe4f static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible||!this.options.toolform_upgrade){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file diff -r 46087ed045d8dbb6570393d5223ba5bd0772b7e4 -r a4f509eb288327415a231c83a79a7aa324d5fe4f templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -11,9 +11,10 @@ params['dataset_id'] = params['id'] self.form_config = controller._build_dict(trans, tool, params) self.form_config.update({ - 'id' : tool.id, - 'job_id' : trans.security.encode_id( job.id ) if job else None, - 'history_id' : trans.security.encode_id( trans.history.id ) + 'id' : tool.id, + 'job_id' : trans.security.encode_id( job.id ) if job else None, + 'history_id' : trans.security.encode_id( trans.history.id ), + 'toolform_upgrade' : trans.app.config.get('toolform_upgrade', False) }) %> ${h.js("libs/bibtex", "libs/jquery/jquery-ui")} 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: natefoo: Update tag latest_2014.10.06 for changeset 011c8b2118be
by commits-noreply＠bitbucket.org 17 Nov '14

17 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1af943ca6e39/ Changeset: 1af943ca6e39 Branch: stable User: natefoo Date: 2014-11-17 15:00:27+00:00 Summary: Update tag latest_2014.10.06 for changeset 011c8b2118be Affected #: 1 file diff -r 011c8b2118be778eaf1ba952730ff876d6447ba9 -r 1af943ca6e39db44bfec74a0debffbf798fc4731 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -e6de07f8c01fe8802282eea1bee326c5efba1b78 latest_2014.10.06 +011c8b2118be778eaf1ba952730ff876d6447ba9 latest_2014.10.06 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fix passing nested parameter replacements to the workflow run API.
by commits-noreply＠bitbucket.org 17 Nov '14

17 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/011c8b2118be/ Changeset: 011c8b2118be Branch: stable User: jmchilton Date: 2014-11-14 17:58:29+00:00 Summary: Fix passing nested parameter replacements to the workflow run API. Thanks to Nicola for finding the problem https://bitbucket.org/galaxy/galaxy-central/commits/fa92c5497232444ade0e704…. Affected #: 3 files diff -r 9c1197f1e259f7925be467f2f6f92fa3e7a5e86c -r 011c8b2118be778eaf1ba952730ff876d6447ba9 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2556,14 +2556,20 @@ history = None value = input.test_param.get_initial_value( trans, context, history=history ) current_case = input.get_current_case( value, trans ) - if current_case != old_current_case: + case_changed = current_case != old_current_case + if case_changed: # Current case has changed, throw away old state group_state = state[input.name] = {} # TODO: we should try to preserve values if we can self.fill_in_new_state( trans, input.cases[current_case].inputs, group_state, context ) group_errors = dict() group_old_errors = dict() - else: + + # If we didn't just change the current case and are coming from HTML - the values + # in incoming represent the old values and should not be replaced. If being updated + # from the API (json) instead of HTML - form values below the current case + # may also be supplied and incoming should be preferred to case defaults. + if (not case_changed) or (source != "html"): # Current case has not changed, update children group_errors = self.update_state( trans, input.cases[current_case].inputs, diff -r 9c1197f1e259f7925be467f2f6f92fa3e7a5e86c -r 011c8b2118be778eaf1ba952730ff876d6447ba9 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -609,7 +609,7 @@ old_errors = state.inputs.pop( "__errors__", {} ) # Update the state step_errors = tool.update_state( trans, tool.inputs, state.inputs, step_updates, - update_only=True, old_errors=old_errors ) + update_only=True, old_errors=old_errors, source="json" ) return state, step_errors def execute( self, trans, progress, invocation, step ): diff -r 9c1197f1e259f7925be467f2f6f92fa3e7a5e86c -r 011c8b2118be778eaf1ba952730ff876d6447ba9 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -111,7 +111,32 @@ param_dict[param_dict['param']] = param_dict['value'] del param_dict[ 'param' ] del param_dict[ 'value' ] - return param_dict + # Inputs can be nested dict, but Galaxy tool code wants nesting of keys (e.g. + # cond1|moo=4 instead of cond1: {moo: 4} ). + new_params = _flatten_step_params( param_dict ) + return new_params + + +def _flatten_step_params( param_dict, prefix="" ): + # TODO: Temporary work around until tool code can process nested data + # structures. This should really happen in there so the tools API gets + # this functionality for free and so that repeats can be handled + # properly. Also the tool code walks the tool inputs so it nows what is + # a complex value object versus something that maps to child parameters + # better than the hack or searching for src and id here. + new_params = {} + keys = param_dict.keys()[:] + for key in keys: + if prefix: + effective_key = "%s|%s" % ( prefix, key ) + else: + effective_key = key + value = param_dict[key] + if isinstance(value, dict) and not ('src' in value and 'id' in value): + new_params.update(_flatten_step_params( value, effective_key) ) + else: + new_params[effective_key] = value + return new_params def build_workflow_run_config( trans, workflow, payload ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: ToolForm: Handle implicit conversion for reruns
by commits-noreply＠bitbucket.org 14 Nov '14

14 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/46087ed045d8/ Changeset: 46087ed045d8 User: guerler Date: 2014-11-14 20:32:29+00:00 Summary: ToolForm: Handle implicit conversion for reruns Affected #: 1 file diff -r 31dbad21bd6b8de1f66db0fe197b713f88e880bc -r 46087ed045d8dbb6570393d5223ba5bd0772b7e4 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2086,15 +2086,17 @@ # add datasets for hda in history.active_datasets_children_and_roles: - if dataset_matcher.hda_match( hda ): + match = dataset_matcher.hda_match( hda ) + if match: + m = match.hda d['options']['hda'].append({ - 'id' : trans.security.encode_id( hda.id ), - 'id_uncoded' : hda.id, - 'hid' : hda.hid, - 'name' : hda.name, + 'id' : trans.security.encode_id( m.id ), + 'id_uncoded' : m.id, + 'hid' : m.hid, + 'name' : m.name, 'src' : 'hda' }) - + # add dataset collections dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) for hdca in history.active_dataset_collections: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Expand HOST_IP in galaxy_infrastructure_url using socket library.
by commits-noreply＠bitbucket.org 14 Nov '14

14 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31dbad21bd6b/ Changeset: 31dbad21bd6b User: jmchilton Date: 2014-11-14 20:23:31+00:00 Summary: Expand HOST_IP in galaxy_infrastructure_url using socket library. Seems to allow dynamically setting correct IP for Galaxy instances inside of Bjoern's docker-in-docker setup (enabling IPython in the stable Galaxy instances). Affected #: 1 file diff -r 96d3d3a4fddeda7bba13d8789f215b684f3a2b09 -r 31dbad21bd6b8de1f66db0fe197b713f88e880bc lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -6,6 +6,8 @@ import os import re +import socket +import string import sys import tempfile import logging @@ -329,6 +331,10 @@ if port: galaxy_infrastructure_url += ":%s" % (port) galaxy_infrastructure_url_set = False + if "HOST_IP" in galaxy_infrastructure_url: + galaxy_infrastructure_url = string.Template(galaxy_infrastructure_url).safe_substitute({ + 'HOST_IP': socket.gethostbyname(socket.gethostname()) + }) self.galaxy_infrastructure_url = galaxy_infrastructure_url self.galaxy_infrastructure_url_set = galaxy_infrastructure_url_set 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: carlfeberhard: History contents API: allow detailed view of HDCA's in index
by commits-noreply＠bitbucket.org 14 Nov '14

14 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/96d3d3a4fdde/ Changeset: 96d3d3a4fdde User: carlfeberhard Date: 2014-11-14 19:41:30+00:00 Summary: History contents API: allow detailed view of HDCA's in index Affected #: 2 files diff -r 7fc0bcc3cdb1e17485035e420d1e0452173cab61 -r 96d3d3a4fddeda7bba13d8789f215b684f3a2b09 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -107,15 +107,21 @@ details = util.listify( details ) for content in history.contents_iter( **contents_kwds ): + encoded_content_id = trans.security.encode_id( content.id ) + detailed = details == 'all' or ( encoded_content_id in details ) + if isinstance( content, trans.app.model.HistoryDatasetAssociation ): - encoded_content_id = trans.security.encode_id( content.id ) - detailed = details == 'all' or ( encoded_content_id in details ) if detailed: rval.append( self._detailed_hda_dict( trans, content ) ) else: rval.append( self._summary_hda_dict( trans, history_id, content ) ) + elif isinstance( content, trans.app.model.HistoryDatasetCollectionAssociation ): - rval.append( self.__collection_dict( trans, content ) ) + if detailed: + rval.append( self.__collection_dict( trans, content, view="element" ) ) + else: + rval.append( self.__collection_dict( trans, content ) ) + return rval #TODO: move to model or Mixin diff -r 7fc0bcc3cdb1e17485035e420d1e0452173cab61 -r 96d3d3a4fddeda7bba13d8789f215b684f3a2b09 templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -147,8 +147,7 @@ linkTarget : 'galaxy_main', $scrollContainer: function(){ return this.$el.parent(); } }); - currPanel - .connectToQuotaMeter( Galaxy.quotaMeter ); + currPanel.connectToQuotaMeter( Galaxy.quotaMeter ); currPanel.loadCurrentHistory(); Galaxy.currHistoryPanel = currPanel; }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Tool test for broken behavior where nested parameter replacements are passed in for a workflow step.
by commits-noreply＠bitbucket.org 14 Nov '14

14 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7fc0bcc3cdb1/ Changeset: 7fc0bcc3cdb1 User: jmchilton Date: 2014-11-14 18:01:10+00:00 Summary: Tool test for broken behavior where nested parameter replacements are passed in for a workflow step. Affected #: 1 file diff -r 596d33e8af919c113028cb943ea2251f9b2bd157 -r 7fc0bcc3cdb1e17485035e420d1e0452173cab61 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -650,12 +650,8 @@ @skip_without_tool( "random_lines1" ) def test_run_replace_params_by_steps( self ): - workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_step_params" ) - workflow_summary_response = self._get( "workflows/%s" % workflow_request[ "workflow_id" ] ) - self._assert_status_code_is( workflow_summary_response, 200 ) - steps = workflow_summary_response.json()[ "steps" ] - last_step_id = str( max( map( int, steps.keys() ) ) ) - params = dumps( { last_step_id: dict( num_lines=5 ) } ) + workflow_request, history_id, steps = self._setup_random_x2_workflow_steps( "test_for_replace_step_params" ) + params = dumps( { str(steps[1]["id"]): dict( num_lines=5 ) } ) workflow_request[ "parameters" ] = params run_workflow_response = self._post( "workflows", data=workflow_request ) self._assert_status_code_is( run_workflow_response, 200 ) @@ -664,6 +660,21 @@ self.__assert_lines_hid_line_count_is( history_id, 2, 8 ) self.__assert_lines_hid_line_count_is( history_id, 3, 5 ) + @skip_without_tool( "random_lines1" ) + def test_run_replace_params_nested( self ): + workflow_request, history_id, steps = self._setup_random_x2_workflow_steps( "test_for_replace_step_params_nested" ) + seed_source = dict( + seed_source_selector="set_seed", + seed="moo", + ) + params = dumps( { str(steps[0]["id"]): dict( num_lines=1, seed_source=seed_source ), + str(steps[1]["id"]): dict( num_lines=1, seed_source=seed_source ) } ) + workflow_request[ "parameters" ] = params + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 200 ) + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + self.assertEquals("3\n", self.dataset_populator.get_history_dataset_content( history_id ) ) + def test_pja_import_export( self ): workflow = self.workflow_populator.load_workflow( name="test_for_pja_import", add_pja=True ) uploaded_workflow_id = self.workflow_populator.create_workflow( workflow ) @@ -774,6 +785,17 @@ ds_map[ key ] = label_map[ label ] return dumps( ds_map ) + def _setup_random_x2_workflow_steps( self, name ): + workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_step_params" ) + random_line_steps = self._random_lines_steps( workflow_request ) + return workflow_request, history_id, random_line_steps + + def _random_lines_steps( self, workflow_request ): + workflow_summary_response = self._get( "workflows/%s" % workflow_request[ "workflow_id" ] ) + self._assert_status_code_is( workflow_summary_response, 200 ) + steps = workflow_summary_response.json()[ "steps" ] + return sorted( filter(lambda step: step["tool_id"] == "random_lines1", steps.values()), key=lambda step: step["id"] ) + def _setup_random_x2_workflow( self, name ): workflow = self.workflow_populator.load_random_x2_workflow( name ) uploaded_workflow_id = self.workflow_populator.create_workflow( workflow ) 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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