4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2d3cbc0bf197/ Changeset: 2d3cbc0bf197 User: natefoo Date: 2015-02-27 16:35:13+00:00 Summary: Add some pointers for developers and deployers in README.rst regarding the Github move. Affected #: 1 file diff -r 8b70692766ec172eb4ac141a5d7266b88526f852 -r 2d3cbc0bf1971ab40a3d0b079aea7f6c48e50f12 README.rst --- a/README.rst +++ b/README.rst @@ -38,7 +38,7 @@ https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies Issues ------- +====== Issues can be submitted to trello via the `galaxyproject website <http://galaxyproject.org/trello/>`__ and viewed on the `Galaxy @@ -51,6 +51,19 @@ Galaxy welcomes new development! There is extensive documentation on developing with Galaxy on the `wiki <https://wiki.galaxyproject.org/Develop>`__. +Source Repository +----------------- + +Galaxy development has moved to `Github +<https://github.com/galaxyproject/galaxy>`__. + +**Developers** should develop against the ``dev`` branch in the Github +repository. + +**Deployers** can continue to pull Galaxy changes from Bitbucket without +interruption. Alternatively, deployers can track the ``master`` branch in +Github. + Syncing a Fork -------------- https://bitbucket.org/galaxy/galaxy-central/commits/097f826b47ee/ Changeset: 097f826b47ee User: martenson Date: 2015-02-27 18:29:05+00:00 Summary: use proper placeholder instead of input value to prevent various search glitches Affected #: 2 files diff -r 2d3cbc0bf1971ab40a3d0b079aea7f6c48e50f12 -r 097f826b47ee3d758e51dbebede467c15f496846 client/galaxy/scripts/templates/tool_search.handlebars --- a/client/galaxy/scripts/templates/tool_search.handlebars +++ b/client/galaxy/scripts/templates/tool_search.handlebars @@ -1,3 +1,3 @@ -<input type="text" name="query" value="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> +<input type="text" name="query" placeholder="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" /><a id="search-clear-btn" title="clear search (esc)"></a> -<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> \ No newline at end of file +<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> diff -r 2d3cbc0bf1971ab40a3d0b079aea7f6c48e50f12 -r 097f826b47ee3d758e51dbebede467c15f496846 static/scripts/templates/tool_search.handlebars --- a/static/scripts/templates/tool_search.handlebars +++ b/static/scripts/templates/tool_search.handlebars @@ -1,3 +1,3 @@ -<input type="text" name="query" value="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> +<input type="text" name="query" placeholder="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" /><a id="search-clear-btn" title="clear search (esc)"></a> -<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> \ No newline at end of file +<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> https://bitbucket.org/galaxy/galaxy-central/commits/99d18d1fa46b/ Changeset: 99d18d1fa46b User: guerler Date: 2015-02-27 18:43:39+00:00 Summary: ToolForm: Make deep copy of current state in order to be on the safe side Affected #: 3 files diff -r 097f826b47ee3d758e51dbebede467c15f496846 -r 99d18d1fa46b506225dad08b0688212c9493edba client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -108,7 +108,7 @@ var new_state = self.tree.finalize(); if (!_.isEqual(new_state, current_state)) { current_state = new_state; - self._updateModel($.extend({}, current_state)); + self._updateModel($.extend(true, {}, current_state)); } }); }); diff -r 097f826b47ee3d758e51dbebede467c15f496846 -r 99d18d1fa46b506225dad08b0688212c9493edba static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -108,7 +108,7 @@ var new_state = self.tree.finalize(); if (!_.isEqual(new_state, current_state)) { current_state = new_state; - self._updateModel($.extend({}, current_state)); + self._updateModel($.extend(true, {}, current_state)); } }); }); diff -r 097f826b47ee3d758e51dbebede467c15f496846 -r 99d18d1fa46b506225dad08b0688212c9493edba static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.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"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(n){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=n&&n.inputs;this._renderForm(n);var m=this.tree.finalize();if(n.initial_errors){this._errors(n)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l._updateModel($.extend({},m))}})});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}})},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$("html, body").animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.id+"/")}})}p.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="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})}); \ 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"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(n){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=n&&n.inputs;this._renderForm(n);var m=this.tree.finalize();if(n.initial_errors){this._errors(n)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l._updateModel($.extend(true,{},m))}})});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}})},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$("html, body").animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.id+"/")}})}p.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="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/179c7c3fbb0d/ Changeset: 179c7c3fbb0d User: natefoo Date: 2015-02-27 19:21:22+00:00 Summary: Fix a typo in datatypes_conf.xml.sample Affected #: 1 file diff -r 99d18d1fa46b506225dad08b0688212c9493edba -r 179c7c3fbb0db10765a97eb632bfc34c570ef0ff config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -180,7 +180,7 @@ <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/><datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/><datatype extension="snpeffdb" type="galaxy.datatypes.text:SnpEffDb" display_in_upload="True"/> - <datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.txt:SnpSiftDbNSFP" display_in_upload="True"/> + <datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.text:SnpSiftDbNSFP" display_in_upload="True"/><datatype extension="dbnsfp.tabular" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"><converter file="tabular_to_dbnsfp.xml" target_datatype="snpsiftdbnsfp"/></datatype> 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.