galaxy-commits November 2014

galaxy-commits@lists.galaxyproject.org

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184 discussions

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d56c63c57bcd/ Changeset: d56c63c57bcd Branch: fix_galaxy_url_parsing User: BjoernGruening Date: 2014-11-24 16:27:10+00:00 Summary: Created new branch fix_galaxy_url_parsing Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/f420fe6e293c/ Changeset: f420fe6e293c Branch: fix_galaxy_url_parsing User: BjoernGruening Date: 2014-11-24 16:28:25+00:00 Summary: getstring() does not exist, use get() instead Affected #: 1 file diff -r d56c63c57bcdaf3abe940495c883b06edb7a72c1 -r f420fe6e293c98bd85da2b092fc34347a769041b lib/galaxy/web/base/interactive_environments.py --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -77,7 +77,7 @@ } if self.attr.viz_config.has_option("docker", "galaxy_url"): - conf_file['galaxy_url'] = self.attr.viz_config.getstring("docker", "galaxy_url") + conf_file['galaxy_url'] = self.attr.viz_config.get("docker", "galaxy_url") elif self.attr.galaxy_config.galaxy_infrastructure_url_set: conf_file['galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/') + '/' else: https://bitbucket.org/galaxy/galaxy-central/commits/c433a83d85cc/ Changeset: c433a83d85cc User: jmchilton Date: 2014-11-24 16:57:42+00:00 Summary: Merged in BjoernGruening/galaxy-central-1/fix_galaxy_url_parsing (pull request #572) Fix bug in IE config parsing. Affected #: 1 file diff -r dd2d0b244a27460ad15df5f12eaf243702086044 -r c433a83d85cc9296b04a51b3cc1225d031ea1b16 lib/galaxy/web/base/interactive_environments.py --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -77,7 +77,7 @@ } if self.attr.viz_config.has_option("docker", "galaxy_url"): - conf_file['galaxy_url'] = self.attr.viz_config.getstring("docker", "galaxy_url") + conf_file['galaxy_url'] = self.attr.viz_config.get("docker", "galaxy_url") elif self.attr.galaxy_config.galaxy_infrastructure_url_set: conf_file['galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/') + '/' else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/475716a95133/ Changeset: 475716a95133 Branch: next-stable User: guerler Date: 2014-11-24 16:50:07+00:00 Summary: ToolForm: Skip new tool form build process if disabled Affected #: 4 files diff -r eeef14ff969c5a8edc9c29912dcd321c8ff6ae87 -r 475716a95133cdeb443f38bbd7fcb7a8291e6069 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 || !this.options.toolform_upgrade) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; diff -r eeef14ff969c5a8edc9c29912dcd321c8ff6ae87 -r 475716a95133cdeb443f38bbd7fcb7a8291e6069 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -324,7 +324,7 @@ }); // switch to classic tool form mako if the form definition is incompatible - if (this.incompatible || !this.options.toolform_upgrade) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; diff -r eeef14ff969c5a8edc9c29912dcd321c8ff6ae87 -r 475716a95133cdeb443f38bbd7fcb7a8291e6069 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(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.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.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(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 diff -r eeef14ff969c5a8edc9c29912dcd321c8ff6ae87 -r 475716a95133cdeb443f38bbd7fcb7a8291e6069 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -1,34 +1,37 @@ <%inherit file="/base.mako"/> -## new tool form -<% - ## TEMPORARY: create tool dictionary in mako while both tool forms are in use. - ## This avoids making two separate requests since the classic form requires the mako anyway. - from galaxy.webapps.galaxy.api.tools import ToolsController - controller = ToolsController(trans.app) - params = dict(trans.request.params) - if 'id' in params: - 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 ), - 'toolform_upgrade' : trans.app.config.get('toolform_upgrade', False) - }) -%> ${h.js("libs/bibtex", "libs/jquery/jquery-ui")} ${h.css('base', 'jquery-ui/smoothness/jquery-ui')} -<script> - require(['mvc/tools/tools-form'], function(ToolsForm){ - $(function(){ - var form = new ToolsForm.View(${ h.dumps(self.form_config) }); + +## skip new tool form code if disabled +%if trans.app.config.get('toolform_upgrade', False): + <% + ## TEMPORARY: create tool dictionary in mako while both tool forms are in use. + ## This avoids making two separate requests since the classic form requires the mako anyway. + from galaxy.webapps.galaxy.api.tools import ToolsController + controller = ToolsController(trans.app) + params = dict(trans.request.params) + if 'id' in params: + 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 ) + }) + %> + <script> + require(['mvc/tools/tools-form'], function(ToolsForm){ + $(function(){ + var form = new ToolsForm.View(${ h.dumps(self.form_config) }); + }); }); - }); -</script> + </script> + <div id="tool-form-classic" style="display: none;"> +%else: + <div id="tool-form-classic"> +%endif -## classic tool form -<div id="tool-form-classic" style="display: none;"><%namespace file="/message.mako" import="render_msg" /><%namespace file="/base_panels.mako" import="overlay" /> https://bitbucket.org/galaxy/galaxy-central/commits/dd2d0b244a27/ Changeset: dd2d0b244a27 User: guerler Date: 2014-11-24 16:50:31+00:00 Summary: Merge Affected #: 4 files diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r dd2d0b244a27460ad15df5f12eaf243702086044 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 || !this.options.toolform_upgrade) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r dd2d0b244a27460ad15df5f12eaf243702086044 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -324,7 +324,7 @@ }); // switch to classic tool form mako if the form definition is incompatible - if (this.incompatible || !this.options.toolform_upgrade) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r dd2d0b244a27460ad15df5f12eaf243702086044 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(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.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.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(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 diff -r 75261cf45d583f8a48172b5209acb24d07fe7b21 -r dd2d0b244a27460ad15df5f12eaf243702086044 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -1,34 +1,37 @@ <%inherit file="/base.mako"/> -## new tool form -<% - ## TEMPORARY: create tool dictionary in mako while both tool forms are in use. - ## This avoids making two separate requests since the classic form requires the mako anyway. - from galaxy.webapps.galaxy.api.tools import ToolsController - controller = ToolsController(trans.app) - params = dict(trans.request.params) - if 'id' in params: - 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 ), - 'toolform_upgrade' : trans.app.config.get('toolform_upgrade', False) - }) -%> ${h.js("libs/bibtex", "libs/jquery/jquery-ui")} ${h.css('base', 'jquery-ui/smoothness/jquery-ui')} -<script> - require(['mvc/tools/tools-form'], function(ToolsForm){ - $(function(){ - var form = new ToolsForm.View(${ h.dumps(self.form_config) }); + +## skip new tool form code if disabled +%if trans.app.config.get('toolform_upgrade', False): + <% + ## TEMPORARY: create tool dictionary in mako while both tool forms are in use. + ## This avoids making two separate requests since the classic form requires the mako anyway. + from galaxy.webapps.galaxy.api.tools import ToolsController + controller = ToolsController(trans.app) + params = dict(trans.request.params) + if 'id' in params: + 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 ) + }) + %> + <script> + require(['mvc/tools/tools-form'], function(ToolsForm){ + $(function(){ + var form = new ToolsForm.View(${ h.dumps(self.form_config) }); + }); }); - }); -</script> + </script> + <div id="tool-form-classic" style="display: none;"> +%else: + <div id="tool-form-classic"> +%endif -## classic tool form -<div id="tool-form-classic" style="display: none;"><%namespace file="/message.mako" import="render_msg" /><%namespace file="/base_panels.mako" import="overlay" /> 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

[galaxyproject/usegalaxy-playbook] a6e699: Updated slide rotation.
by GitHub 23 Nov '14

23 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a6e69901bee143ea0516e94847ef0ab0dc60acd3 https://github.com/galaxyproject/usegalaxy-playbook/commit/a6e69901bee143ea… Author: Dave Clements <clements(a)Clements-Galaxy.local> Date: 2014-11-22 (Sat, 22 Nov 2014) Changed paths: A files/galaxy/common/static/welcome_img/CoSSci.png M files/galaxy/common/static/welcome_img/GCC2015SaveTheseDates.png A files/galaxy/common/static/welcome_img/GalaxyIFBDay2014.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation.

1 0

[galaxyproject/usegalaxy-playbook] fb4f56: Update Main.
by GitHub 20 Nov '14

20 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fb4f561bcb5ef21c4e6b30dabf71b41c8f58a0d2 https://github.com/galaxyproject/usegalaxy-playbook/commit/fb4f561bcb5ef21c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-11-20 (Thu, 20 Nov 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/af67ea0dd4d5/ Changeset: af67ea0dd4d5 Branch: next-stable User: guerler Date: 2014-11-20 19:29:27+00:00 Summary: Fix boolean handling for workflow editor Affected #: 1 file diff -r b87a9309cc68f7bffe886123b083d058c6347144 -r af67ea0dd4d5c718906ad883c76fd1efce86dbfc lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -126,9 +126,6 @@ def is_checked( value ): if value == True: return True - if isinstance( value, basestring ): - if value.lower() in [ "yes", "true", "on" ]: - return True # This may look strange upon initial inspection, but see the comments in the get_html() method # above for clarification. Basically, if value is not True, then it will always be a list with # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not https://bitbucket.org/galaxy/galaxy-central/commits/9dae58e22285/ Changeset: 9dae58e22285 User: guerler Date: 2014-11-20 19:29:44+00:00 Summary: Merge Affected #: 1 file diff -r 179f809b70dfabff53a6731ab70af949bc213e07 -r 9dae58e2228516766b65058b86d949bcfb23f775 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -126,9 +126,6 @@ def is_checked( value ): if value == True: return True - if isinstance( value, basestring ): - if value.lower() in [ "yes", "true", "on" ]: - return True # This may look strange upon initial inspection, but see the comments in the get_html() method # above for clarification. Basically, if value is not True, then it will always be a list with # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not 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: natefoo: Update tag latest_2014.10.06 for changeset bb79e87274d7
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cae8a513079a/ Changeset: cae8a513079a Branch: stable User: natefoo Date: 2014-11-20 19:00:30+00:00 Summary: Update tag latest_2014.10.06 for changeset bb79e87274d7 Affected #: 1 file diff -r bb79e87274d7ef4e043a84aeef8516a5418ef3b6 -r cae8a513079a183d16bd8a16b915d6aa5322a249 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06 +bb79e87274d7ef4e043a84aeef8516a5418ef3b6 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.

1 0

[galaxyproject/usegalaxy-playbook] 816d86: Update Main.
by GitHub 20 Nov '14

20 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 816d866a3f8b8abc20d2e0f110156ea70e5acf3e https://github.com/galaxyproject/usegalaxy-playbook/commit/816d866a3f8b8abc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-11-20 (Thu, 20 Nov 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b87a9309cc68/ Changeset: b87a9309cc68 Branch: next-stable User: jmchilton Date: 2014-11-13 14:19:51+00:00 Summary: Allow resolution of relative paths in tool data configuration and loc files. The string ${__HERE__} will be expanded out to the directory the file (XML configuration or loc) currently resides in. Along with some changes to planemo to detect test data files (https://github.com/galaxyproject/planemo/commit/a40130417dc1be2da785cd5dff6…) - the following picard tweak demonstrates how tool developers could use this to build test cases for cached/index data (https://github.com/jmchilton/picard/commit/4df8974384081ee1bb0f97e1bb8d7f93…). Affected #: 1 file diff -r 20def6edca5958f029beae47b4a5cffc9fae8f3d -r b87a9309cc68f7bffe886123b083d058c6347144 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -10,6 +10,7 @@ import os import os.path import shutil +import string import tempfile from galaxy import util @@ -71,7 +72,7 @@ tree = util.parse_xml( filename ) root = tree.getroot() for table_elem in root.findall( 'table' ): - table = ToolDataTable.from_elem( table_elem, tool_data_path, from_shed_config ) + table = ToolDataTable.from_elem( table_elem, tool_data_path, from_shed_config, filename=filename ) table_elems.append( table_elem ) if table.name not in self.data_tables: self.data_tables[ table.name ] = table @@ -167,16 +168,17 @@ class ToolDataTable( object ): @classmethod - def from_elem( cls, table_elem, tool_data_path, from_shed_config ): + def from_elem( cls, table_elem, tool_data_path, from_shed_config, filename ): table_type = table_elem.get( 'type', 'tabular' ) assert table_type in tool_data_table_types, "Unknown data table type '%s'" % type - return tool_data_table_types[ table_type ]( table_elem, tool_data_path, from_shed_config=from_shed_config ) + return tool_data_table_types[ table_type ]( table_elem, tool_data_path, from_shed_config=from_shed_config, filename=filename ) - def __init__( self, config_element, tool_data_path, from_shed_config = False): + def __init__( self, config_element, tool_data_path, from_shed_config = False, filename=None ): self.name = config_element.get( 'name' ) self.comment_char = config_element.get( 'comment_char' ) self.empty_field_value = config_element.get( 'empty_field_value', '' ) self.empty_field_values = {} + self.here = filename and os.path.dirname(filename) self.filenames = odict() self.tool_data_path = tool_data_path self.missing_index_file = None @@ -241,8 +243,8 @@ type_key = 'tabular' - def __init__( self, config_element, tool_data_path, from_shed_config = False): - super( TabularToolDataTable, self ).__init__( config_element, tool_data_path, from_shed_config) + def __init__( self, config_element, tool_data_path, from_shed_config = False, filename=None ): + super( TabularToolDataTable, self ).__init__( config_element, tool_data_path, from_shed_config, filename) self.config_element = config_element self.data = [] self.configure_and_load( config_element, tool_data_path, from_shed_config) @@ -265,7 +267,7 @@ repo_info = None # Read every file for file_element in config_element.findall( 'file' ): - filename = file_path = file_element.get( 'path', None ) + filename = file_path = expand_here_template( file_element.get( 'path', None ), here=self.here ) found = False if file_path is None: log.debug( "Encountered a file element (%s) that does not contain a path value when loading tool data table '%s'.", util.xml_to_string( file_element ), self.name ) @@ -300,7 +302,7 @@ errors = [] if found: - self.data.extend( self.parse_file_fields( open( filename ), errors=errors ) ) + self.extend_data_with( filename, errors=errors ) self._update_version() else: self.missing_index_file = filename @@ -326,7 +328,7 @@ def handle_found_index_file( self, filename ): self.missing_index_file = None - self.data.extend( self.parse_file_fields( open( filename ) ) ) + self.extend_data_with( filename ) def get_fields( self ): return self.data @@ -380,7 +382,11 @@ if 'name' not in self.columns: self.columns['name'] = self.columns['value'] - def parse_file_fields( self, reader, errors=None ): + def extend_data_with( self, filename, errors=None ): + here = os.path.dirname(os.path.abspath(filename)) + self.data.extend( self.parse_file_fields( open( filename ), errors=errors, here=here ) ) + + def parse_file_fields( self, reader, errors=None, here="__HERE__" ): """ Parse separated lines from file and return a list of tuples. @@ -394,6 +400,7 @@ continue line = line.rstrip( "\n\r" ) if line: + line = expand_here_template( line, here=here ) fields = line.split( self.separator ) if self.largest_index < len( fields ): rval.append( fields ) @@ -529,5 +536,12 @@ rval['fields'] = self.get_fields() return rval + +def expand_here_template(content, here=None): + if here and content: + content = string.Template(content).safe_substitute( { "__HERE__": here }) + return content + + # Registry of tool data types by type_key tool_data_table_types = dict( [ ( cls.type_key, cls ) for cls in [ TabularToolDataTable ] ] ) https://bitbucket.org/galaxy/galaxy-central/commits/179f809b70df/ Changeset: 179f809b70df User: jmchilton Date: 2014-11-20 16:31:34+00:00 Summary: Merge next-stable. 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/20def6edca59/ Changeset: 20def6edca59 Branch: next-stable User: jmchilton Date: 2014-11-20 16:21:25+00:00 Summary: Merge stable into next-stable. Affected #: 3 files diff -r 30e0e657a607b406b899a88d8612d3b6a6602ed6 -r 20def6edca5958f029beae47b4a5cffc9fae8f3d .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -011c8b2118be778eaf1ba952730ff876d6447ba9 latest_2014.10.06 +acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06 diff -r 30e0e657a607b406b899a88d8612d3b6a6602ed6 -r 20def6edca5958f029beae47b4a5cffc9fae8f3d lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -403,6 +403,7 @@ dataset.warnings = [] dataset.metadata = {} dataset.composite_files = {} + dataset.uuid = None #load metadata files_metadata = context.get( self.metadata_ref, {} ) metadata_name_substition_default_dict = dict( [ ( composite_file.substitute_name_with_metadata, d_type.metadata_spec[ composite_file.substitute_name_with_metadata ].default ) for composite_file in d_type.composite_files.values() if composite_file.substitute_name_with_metadata ] ) diff -r 30e0e657a607b406b899a88d8612d3b6a6602ed6 -r 20def6edca5958f029beae47b4a5cffc9fae8f3d lib/pulsar/client/transport/standard.py --- a/lib/pulsar/client/transport/standard.py +++ b/lib/pulsar/client/transport/standard.py @@ -24,11 +24,13 @@ input = None try: if input_path: - if getsize(input_path): + size = getsize(input_path) + if size: input = open(input_path, 'rb') data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) else: data = b"" + request.add_header('Content-Length', str(size)) response = self._url_open(request, data) finally: if input: https://bitbucket.org/galaxy/galaxy-central/commits/81dc20496497/ Changeset: 81dc20496497 User: jmchilton Date: 2014-11-20 16:21:42+00:00 Summary: Merge next-stable into default. Affected #: 3 files diff -r 3ec1e82f0fbde4d2cfb390acb4548474ff48d1a9 -r 81dc204964973c94bdee8631fb806a6214574336 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -011c8b2118be778eaf1ba952730ff876d6447ba9 latest_2014.10.06 +acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06 diff -r 3ec1e82f0fbde4d2cfb390acb4548474ff48d1a9 -r 81dc204964973c94bdee8631fb806a6214574336 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -403,6 +403,7 @@ dataset.warnings = [] dataset.metadata = {} dataset.composite_files = {} + dataset.uuid = None #load metadata files_metadata = context.get( self.metadata_ref, {} ) metadata_name_substition_default_dict = dict( [ ( composite_file.substitute_name_with_metadata, d_type.metadata_spec[ composite_file.substitute_name_with_metadata ].default ) for composite_file in d_type.composite_files.values() if composite_file.substitute_name_with_metadata ] ) diff -r 3ec1e82f0fbde4d2cfb390acb4548474ff48d1a9 -r 81dc204964973c94bdee8631fb806a6214574336 lib/pulsar/client/transport/standard.py --- a/lib/pulsar/client/transport/standard.py +++ b/lib/pulsar/client/transport/standard.py @@ -24,11 +24,13 @@ input = None try: if input_path: - if getsize(input_path): + size = getsize(input_path) + if size: input = open(input_path, 'rb') data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ) else: data = b"" + request.add_header('Content-Length', str(size)) response = self._url_open(request, data) finally: if input: 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 20 Nov '14

20 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/30e0e657a607/ Changeset: 30e0e657a607 Branch: next-stable User: carlfeberhard Date: 2014-11-20 15:31:05+00:00 Summary: History, view multiple: show error when anonymous with links to register and log in Affected #: 1 file diff -r c3ac0d1c84e71e49d04b5ddb2644415111605cbc -r 30e0e657a607b406b899a88d8612d3b6a6602ed6 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -609,6 +609,14 @@ def view_multiple( self, trans, include_deleted_histories=False, order='update' ): """ """ + if not trans.user: + log_in_url = url_for( controller="user", action="login", use_panels=True ) + log_in_link = "<a href='%s'>log in</a>" % ( log_in_url ) + register_url = url_for( controller="user", action="create", use_panels=True ) + register_link = "<a href='%s'>register</a>" % ( register_url ) + return trans.show_error_message( "You need to %s or %s to use multiple histories" + % ( log_in_link, register_link ), use_panels=True ) + #TODO: allow specifying user_id for admin? include_deleted_histories = galaxy.util.string_as_bool( include_deleted_histories ) order = order if order in ( 'update', 'name', 'size' ) else 'update' https://bitbucket.org/galaxy/galaxy-central/commits/3ec1e82f0fbd/ Changeset: 3ec1e82f0fbd User: carlfeberhard Date: 2014-11-20 15:31:32+00:00 Summary: Merge next-stable Affected #: 1 file diff -r a88cc74c931780f08c9858ac25c3c03324084135 -r 3ec1e82f0fbde4d2cfb390acb4548474ff48d1a9 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -609,6 +609,14 @@ def view_multiple( self, trans, include_deleted_histories=False, order='update' ): """ """ + if not trans.user: + log_in_url = url_for( controller="user", action="login", use_panels=True ) + log_in_link = "<a href='%s'>log in</a>" % ( log_in_url ) + register_url = url_for( controller="user", action="create", use_panels=True ) + register_link = "<a href='%s'>register</a>" % ( register_url ) + return trans.show_error_message( "You need to %s or %s to use multiple histories" + % ( log_in_link, register_link ), use_panels=True ) + #TODO: allow specifying user_id for admin? include_deleted_histories = galaxy.util.string_as_bool( include_deleted_histories ) order = order if order in ( 'update', 'name', 'size' ) else 'update' 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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galaxy-commits November 2014