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20 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/66f79fabe38d/
Changeset: 66f79fabe38d
Branch: release_15.03
User: guerler
Date: 2015-02-28 06:33:15+00:00
Summary: ToolForm: Update biostar url for tool search
Affected #: 3 files
diff -r fe4cfbd300a11b8fc1f05fff06209035f0ef26e6 -r 66f79fabe38de9641392138aed4717afe0180f21 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
@@ -230,7 +230,7 @@
title : 'Search',
tooltip : 'Search help for this tool (Biostar)',
onclick : function() {
- window.open(options.biostar_url + '/t/' + options.id + '/');
+ window.open(options.biostar_url + '/local/search/page/?q=' + options.name);
}
});
};
diff -r fe4cfbd300a11b8fc1f05fff06209035f0ef26e6 -r 66f79fabe38de9641392138aed4717afe0180f21 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
@@ -230,7 +230,7 @@
title : 'Search',
tooltip : 'Search help for this tool (Biostar)',
onclick : function() {
- window.open(options.biostar_url + '/t/' + options.id + '/');
+ window.open(options.biostar_url + '/local/search/page/?q=' + options.name);
}
});
};
diff -r fe4cfbd300a11b8fc1f05fff06209035f0ef26e6 -r 66f79fabe38de9641392138aed4717afe0180f21 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($.extend(true,{},m))}})});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}})},reciept:function(l){$(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
+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+"/local/search/page/?q="+t.name)}})}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/39d8e73660e6/
Changeset: 39d8e73660e6
Branch: release_15.03
User: guerler
Date: 2015-02-28 09:30:14+00:00
Summary: ToolForm: Do not show submission error if user closes progress modal
Affected #: 3 files
diff -r 66f79fabe38de9641392138aed4717afe0180f21 -r 39d8e73660e641279d5089b268ebe35de46baf89 client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -34,7 +34,13 @@
console.debug(job_def);
// show progress modal
- this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: { 'Close' : function () {self.app.modal.hide();} }});
+ var user_is_waiting = true;
+ this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
+ 'Close' : function () {
+ self.app.modal.hide();
+ user_is_waiting = false;
+ }
+ }});
// post job
Utils.request({
@@ -57,7 +63,7 @@
} else {
// show error message with details
console.debug(response);
- self.app.modal.show({
+ user_is_waiting && self.app.modal.show({
title : 'Job submission failed',
body : ToolTemplate.error(job_def),
buttons : {
diff -r 66f79fabe38de9641392138aed4717afe0180f21 -r 39d8e73660e641279d5089b268ebe35de46baf89 static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -34,7 +34,13 @@
console.debug(job_def);
// show progress modal
- this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: { 'Close' : function () {self.app.modal.hide();} }});
+ var user_is_waiting = true;
+ this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
+ 'Close' : function () {
+ self.app.modal.hide();
+ user_is_waiting = false;
+ }
+ }});
// post job
Utils.request({
@@ -57,7 +63,7 @@
} else {
// show error message with details
console.debug(response);
- self.app.modal.show({
+ user_is_waiting && self.app.modal.show({
title : 'Job submission failed',
body : ToolTemplate.error(job_def),
buttons : {
diff -r 66f79fabe38de9641392138aed4717afe0180f21 -r 39d8e73660e641279d5089b268ebe35de46baf89 static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var d={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.reciept(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c.app.highlight(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var e={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(e)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(e);var d=true;this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide();d=false}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:e,success:function(f){c.app.modal.hide();c.app.reciept(a.success(f));c._refreshHdas()},error:function(f,h){c.app.modal.hide();if(f&&f.message&&f.message.data){var i=c.app.tree.matchResponse(f.message.data);for(var g in i){c.app.highlight(g,i[g]);break}}else{console.debug(f);d&&c.app.modal.show({title:"Job submission failed",body:a.error(e),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/1971a31f450f/
Changeset: 1971a31f450f
Branch: release_15.03
User: guerler
Date: 2015-02-28 09:37:37+00:00
Summary: ToolForm: Use default closing behaviour for progress modal
Affected #: 3 files
diff -r 39d8e73660e641279d5089b268ebe35de46baf89 -r 1971a31f450f1dde718f096d5001b7dfdf4ccfbd client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -35,7 +35,7 @@
// show progress modal
var user_is_waiting = true;
- this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
+ this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: {
'Close' : function () {
self.app.modal.hide();
user_is_waiting = false;
diff -r 39d8e73660e641279d5089b268ebe35de46baf89 -r 1971a31f450f1dde718f096d5001b7dfdf4ccfbd static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -35,7 +35,7 @@
// show progress modal
var user_is_waiting = true;
- this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
+ this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: {
'Close' : function () {
self.app.modal.hide();
user_is_waiting = false;
diff -r 39d8e73660e641279d5089b268ebe35de46baf89 -r 1971a31f450f1dde718f096d5001b7dfdf4ccfbd static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var e={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(e)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(e);var d=true;this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide();d=false}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:e,success:function(f){c.app.modal.hide();c.app.reciept(a.success(f));c._refreshHdas()},error:function(f,h){c.app.modal.hide();if(f&&f.message&&f.message.data){var i=c.app.tree.matchResponse(f.message.data);for(var g in i){c.app.highlight(g,i[g]);break}}else{console.debug(f);d&&c.app.modal.show({title:"Job submission failed",body:a.error(e),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var e={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(e)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(e);var d=true;this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide();d=false}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:e,success:function(f){c.app.modal.hide();c.app.reciept(a.success(f));c._refreshHdas()},error:function(f,h){c.app.modal.hide();if(f&&f.message&&f.message.data){var i=c.app.tree.matchResponse(f.message.data);for(var g in i){c.app.highlight(g,i[g]);break}}else{console.debug(f);d&&c.app.modal.show({title:"Job submission failed",body:a.error(e),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/ba09b6d65655/
Changeset: ba09b6d65655
Branch: release_15.03
User: guerler
Date: 2015-02-28 17:12:10+00:00
Summary: Charts: Add data point labels to all nvd3 charts (without this gene expression analysis using scatter plots is not very useful)
Affected #: 6 files
diff -r 1971a31f450f1dde718f096d5001b7dfdf4ccfbd -r ba09b6d6565592cb67bd08aec844ea7c8da50c94 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors
// Underscore may be freely distributed under the MIT license.
-define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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e.length>0?e.val():null},wait:function(){this._size()==0&&(this._messageShow(this.options.wait_text,"info"),this.$options.hide(),this.$menu.hide())},unwait:function(){this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.error_text,"danger"),this.$options.hide(),this.$menu.hide()):(this._messageHide(),this.$options.css("display","inline-block"),this.$menu.show());if(this.select_button){var e=this._size(),t=this._getValue();t instanceof Array?t.length!==e?this.select_button.value(1):this.select_button.value(2):this.select_button.value(0)}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push($(this).val())}),e.validate(t)?this.options.multiple?t:t[0]:null},_size:function(){return this.$(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert 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no-padding");var n='<label class="btn btn-default">';return e.icon&&(n+='<i class="'+t+'"/>'),n+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>',e.label&&(n+=e.label),n+="</label>",n},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Base:n,BaseIcons:r,Radio:i,RadioButton:o,Checkbox:s}}),define("mvc/ui/ui-drilldown",["utils/utils","mvc/ui/ui-options"],function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple=e.display=="checkbox",t.BaseIcons.prototype.initialize.call(this,e),this.initial=!0},value:function(e){var n=t.BaseIcons.prototype.value.call(this,e);if(this.initial&&n!==null&&this.header_index){this.initial=!1;var r=n;$.isArray(r)||(r=[r]);for(var i in r){var s=this.header_index[r[i]];for(var o in s)this._setState(s[o],!0)}}return n},_setState:function(e,t){var n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div 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r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&!o.is_text&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=r.is_text,c=[],h=n[e];o&&c.push({label:"Column: Row Number",value:"auto"}),f&&c.push({label:"Column: None",value:"zero"});var p=t.metadata_column_types;for(var d in p){var v=!1;p[d]=="int"||p[d]=="float"?v=u:v=l||s,v&&c.push({label:"Column: "+(parseInt(d)+1),value:d})}h.update(c),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!h.exists(this.group.get(e))){var m=h.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+m+'".'),this.group.set(e,m)}h.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){h.value(i.group.get(e))}),h.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),h.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var 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t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return arguments.length?(n=e,g):n},g.height=function(e){return arguments.length?(r=e,g):r},g.clipEdge=function(e){return arguments.length?(h=e,g):h},g.color=function(t){return arguments.length?(i=e.utils.getColor(t),g):i},g.offset=function(e){return arguments.length?(f=e,g):f},g.order=function(e){return arguments.length?(l=e,g):l},g.style=function(e){if(!arguments.length)return a;a=e;switch(a){case"stack":g.offset("zero"),g.order("default");break;case"stream":g.offset("wiggle"),g.order("inside-out");break;case"stream-center":g.offset("silhouette"),g.order("inside-out");break;case"expand":g.offset("expand"),g.order("default");break;case"stack_percent":g.offset(g.d3_stackedOffset_stackPercent),g.order("default")}return g},g.interpolate=function(e){return arguments.length?(c=e,g):c},g},e.models.stackedAreaChart=function(){function M(y){return y.each(function(y){var 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k.indexOf(e.metaKey)!==-1}),s.width(C).color(["#444","#444","#444"]),I.select(".nv-controlsWrap").datum(R).call(s),u.top!=Math.max(s.height(),i.height())&&(u.top=Math.max(s.height(),i.height()),P=(f||parseInt(A.style("height"))||400)-u.top-u.bottom),I.select(".nv-controlsWrap").attr("transform","translate(0,"+ -u.top+")")}j.attr("transform","translate("+u.left+","+u.top+")"),v&&I.select(".nv-y.nv-axis").attr("transform","translate("+D+",0)"),m&&(o.width(D).height(P).margin({left:u.left,top:u.top}).svgContainer(A).xScale(b),j.select(".nv-interactive").call(o)),t.width(D).height(P);var U=I.select(".nv-stackedWrap").datum(y);U.call(t),p&&(n.scale(b).ticks(D/100).tickSize(-P,0),I.select(".nv-x.nv-axis").attr("transform","translate(0,"+P+")"),I.select(".nv-x.nv-axis").call(n)),d&&(r.scale(w).ticks(t.offset()=="wiggle"?0:P/36).tickSize(-D,0).setTickFormat(t.style()=="expand"||t.style()=="stack_percent"?d3.format("%"):E),I.select(".nv-y.nv-axis").call(r)),t.dispatch.on("areaClick.toggle",function(e){y.filter(function(e){return!e.disabled}).length===1?y.forEach(function(e){e.disabled=!1}):y.forEach(function(t,n){t.disabled=n!=e.seriesIndex}),S.disabled=y.map(function(e){return!!e.disabled}),N.stateChange(S),M.update()}),i.dispatch.on("stateChange",function(e){S.disabled=e.disabled,N.stateChange(S),M.update()}),s.dispatch.on("legendClick",function(e,n){if(!e.disabled)return;R=R.map(function(e){return e.disabled=!0,e}),e.disabled=!1,t.style(e.style),S.style=t.style(),N.stateChange(S),M.update()}),o.dispatch.on("elementMousemove",function(i){t.clearHighlights();var s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return r.tickFormat()(e)};o.tooltip.position({left:f+u.left,top:i.mouseY+u.top}).chartContainer(_.parentNode).enabled(g).valueFormatter(m).data({value:v,series:c})(),o.renderGuideLine(f)}),o.dispatch.on("elementMouseout",function(e){N.tooltipHide(),t.clearHighlights()}),N.on("tooltipShow",function(e){g&&O(e,_.parentNode)}),N.on("changeState",function(e){typeof e.disabled!="undefined"&&y.length===e.disabled.length&&(y.forEach(function(t,n){t.disabled=e.disabled[n]}),S.disabled=e.disabled),typeof e.style!="undefined"&&t.style(e.style),M.update()})}),M}var t=e.models.stackedArea(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.interactiveGuideline(),u={top:30,right:25,bottom:50,left:60},a=null,f=null,l=e.utils.defaultColor(),c=!0,h=!0,p=!0,d=!0,v=!1,m=!1,g=!0,y=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" on "+t+"</p>"},b,w,E=d3.format(",.2f"),S={style:t.style()},x=null,T="No Data Available.",N=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),C=250,k=["Stacked","Stream","Expanded"],L={},A=0;n.orient("bottom").tickPadding(7),r.orient(v?"right":"left"),s.updateState(!1);var O=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),a=n.tickFormat()(t.x()(i.point,i.pointIndex)),f=r.tickFormat()(t.y()(i.point,i.pointIndex)),l=y(i.series.key,a,f,i,M);e.tooltip.show([o,u],l,i.value<0?"n":"s",null,s)};return t.dispatch.on("tooltipShow",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],N.tooltipShow(e)}),t.dispatch.on("tooltipHide",function(e){N.tooltipHide(e)}),N.on("tooltipHide",function(){g&&e.tooltip.cleanup()}),M.dispatch=N,M.stacked=t,M.legend=i,M.controls=s,M.xAxis=n,M.yAxis=r,M.interactiveLayer=o,d3.rebind(M,t,"x","y","size","xScale","yScale","xDomain","yDomain","xRange","yRange","sizeDomain","interactive","useVoronoi","offset","order","style","clipEdge","forceX","forceY","forceSize","interpolate"),M.options=e.utils.optionsFunc.bind(M),M.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,M):u},M.width=function(e){return arguments.length?(a=e,M):a},M.height=function(e){return arguments.length?(f=e,M):f},M.color=function(n){return arguments.length?(l=e.utils.getColor(n),i.color(l),t.color(l),M):l},M.showControls=function(e){return arguments.length?(c=e,M):c},M.showLegend=function(e){return arguments.length?(h=e,M):h},M.showXAxis=function(e){return arguments.length?(p=e,M):p},M.showYAxis=function(e){return arguments.length?(d=e,M):d},M.rightAlignYAxis=function(e){return arguments.length?(v=e,r.orient(e?"right":"left"),M):v},M.useInteractiveGuideline=function(e){return arguments.length?(m=e,e===!0&&(M.interactive(!1),M.useVoronoi(!1)),M):m},M.tooltip=function(e){return arguments.length?(y=e,M):y},M.tooltips=function(e){return arguments.length?(g=e,M):g},M.tooltipContent=function(e){return arguments.length?(y=e,M):y},M.state=function(e){return arguments.length?(S=e,M):S},M.defaultState=function(e){return arguments.length?(x=e,M):x},M.noData=function(e){return arguments.length?(T=e,M):T},M.transitionDuration=function(e){return arguments.length?(A=e,M):A},M.controlsData=function(e){return arguments.length?(k=e,M):k},M.controlLabels=function(e){return arguments.length?typeof e!="object"?L:(L=e,M):L},r.setTickFormat=r.tickFormat,r.tickFormat=function(e){return arguments.length?(E=e,r):E},M}}(),define("plugin/plugins/nvd3/nv.d3",function(){}),define("plugin/charts/nvd3/common/config",["plugin/charts/forms/default","plugin/plugins/nvd3/nv.d3"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"NVD3",tag:"svg",keywords:"small",columns:{tooltip:{title:"Data point labels",is_text:!0,is_numeric:!0,is_auto:!0}}})}),define("plugin/charts/nvd3/bar/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/bar_stacked/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/bar_horizontal/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}},columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/bar_horizontal_stacked/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}},columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/line_focus/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus",category:"Others",zoomable:"native",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/pie/config",["plugin/plugins/nvd3/nv.d3"],function(){return $.extend(!0,{},{title:"Pie chart",category:"Area charts",library:"NVD3",tag:"svg",keywords:"small",columns:{label:{title:"Labels",is_label:!0,is_auto:!0},y:{title:"Values",is_numeric:!0}},settings:{main_separator:{type:"separator",title:"Pie chart settings"},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{init:"true",hide:!0}}})}),define("plugin/charts/nvd3/stackedarea_full/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea_stream/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts",zoomable:!0,keywords:"default small",showmaxmin:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/histogram/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{x_axis_label:{init:"Values"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_precision:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/scatter/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","utils/deferred","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})});
\ No newline at end of file
diff -r 1971a31f450f1dde718f096d5001b7dfdf4ccfbd -r ba09b6d6565592cb67bd08aec844ea7c8da50c94 config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
@@ -4,7 +4,15 @@
category : '',
library : 'NVD3',
tag : 'svg',
- keywords : 'small'
+ keywords : 'small',
+ columns : {
+ tooltip : {
+ title : 'Data point labels',
+ is_text : true,
+ is_numeric : true,
+ is_auto : true
+ }
+ }
});
});
\ No newline at end of file
diff -r 1971a31f450f1dde718f096d5001b7dfdf4ccfbd -r ba09b6d6565592cb67bd08aec844ea7c8da50c94 config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
@@ -15,71 +15,76 @@
options.render = function(canvas_id, groups) {
return self.render(canvas_id, groups)
};
-
+
// call panel helper
Tools.panelHelper(app, options);
},
-
+
// render
render : function(canvas_id, groups) {
var chart = this.options.chart;
var type = this.options.type;
var makeConfig = this.options.makeConfig;
-
+
// create nvd3 model
var d3chart = nv.models[type]()
-
+
// request data
var self = this;
nv.addGraph(function() {
try {
// x axis label
d3chart.xAxis.axisLabel(chart.settings.get('x_axis_label'));
-
+
// y axis label
d3chart.yAxis.axisLabel(chart.settings.get('y_axis_label'))
.axisLabelDistance(30);
-
+
// controls
d3chart.options({showControls: false});
-
+
// legend
if (d3chart.showLegend) {
d3chart.showLegend(chart.settings.get('show_legend') == 'true');
}
-
+
// make categories
self._makeAxes(d3chart, groups, chart.settings);
-
+
// custom callback
if (makeConfig) {
makeConfig(d3chart);
}
-
+
// hide controls if in multi-viewer mode
if (chart.settings.get('use_panels') === 'true') {
d3chart.options({showControls: false});
}
-
+
// hide min/max values
d3chart.xAxis.showMaxMin(false);
d3chart.yAxis.showMaxMin(chart.definition.showmaxmin);
-
+
+ // configure tooltips
+ d3chart.tooltipContent(function(key, x, y, graph) {
+ return '<h3>' + (graph.point.tooltip || key) + '</h3>';
+ });
+
// draw chart
if ($('#' + canvas_id).length == 0) {
return;
}
var canvas = d3.select('#' + canvas_id);
- canvas.datum(groups)
+ canvas.datum(groups)
.call(d3chart);
-
+
// add zoom/pan handler
if (chart.definition.zoomable && chart.definition.zoomable != 'native') {
// clip edges
if (d3chart.clipEdge) {
d3chart.clipEdge(true);
}
-
+
// add zoom
Tools.addZoom({
xAxis : d3chart.xAxis,
@@ -97,16 +102,16 @@
self._handleError(chart, err);
}
});
-
+
// return
return true;
},
-
+
// create axes formatting
_makeAxes: function(d3chart, groups, settings) {
// result
var categories = Tools.makeCategories(groups);
-
+
// make axes
function makeTickFormat (id) {
Tools.makeTickFormat({
@@ -125,7 +130,7 @@
makeTickFormat('x');
makeTickFormat('y');
},
-
+
// handle error
_handleError: function(chart, err) {
chart.state('failed', err);
diff -r 1971a31f450f1dde718f096d5001b7dfdf4ccfbd -r ba09b6d6565592cb67bd08aec844ea7c8da50c94 config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
@@ -6,11 +6,11 @@
zoomable : true,
columns : {
x : {
- title : 'Values for x-axis',
+ title : 'Values for x-axis',
is_numeric : true
},
y : {
- title : 'Values for y-axis',
+ title : 'Values for y-axis',
is_numeric : true
}
}
diff -r 1971a31f450f1dde718f096d5001b7dfdf4ccfbd -r ba09b6d6565592cb67bd08aec844ea7c8da50c94 config/plugins/visualizations/charts/static/library/datasets.js
--- a/config/plugins/visualizations/charts/static/library/datasets.js
+++ b/config/plugins/visualizations/charts/static/library/datasets.js
@@ -299,7 +299,7 @@
// get/fix value
var v = column_data[j];
- if (isNaN(v) && !column.is_label) {
+ if (isNaN(v) && !column.is_label && !column.is_text) {
v = 0;
}
diff -r 1971a31f450f1dde718f096d5001b7dfdf4ccfbd -r ba09b6d6565592cb67bd08aec844ea7c8da50c94 config/plugins/visualizations/charts/static/views/group.js
--- a/config/plugins/visualizations/charts/static/views/group.js
+++ b/config/plugins/visualizations/charts/static/views/group.js
@@ -145,12 +145,13 @@
// link this
var self = this;
- // is a numeric number required
+ // available column options
var is_label = column_definition.is_label;
var is_auto = column_definition.is_auto;
var is_numeric = column_definition.is_numeric;
var is_unique = column_definition.is_unique;
var is_zero = column_definition.is_zero;
+ var is_text = column_definition.is_text;
// configure columns
var columns = [];
@@ -182,7 +183,7 @@
if (meta[key] == 'int' || meta[key] == 'float') {
valid = is_numeric;
} else {
- valid = is_label;
+ valid = is_text || is_label;
}
// check type
https://bitbucket.org/galaxy/galaxy-central/commits/c0eef4e23819/
Changeset: c0eef4e23819
Branch: release_15.03
User: jmchilton
Date: 2015-03-02 18:45:12+00:00
Summary: Update basic.py to allow collection reduction with new tool form.
Affected #: 1 file
diff -r ba09b6d6565592cb67bd08aec844ea7c8da50c94 -r c0eef4e238198d40654404bc3baa2ec2e9565a1c lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1987,10 +1987,19 @@
value = [ int( value_part ) for value_part in value.split( "," ) ]
if isinstance( value, list ):
rval = []
+ found_hdca = False
for single_value in value:
- if isinstance( single_value, dict ):
- assert single_value['src'] == 'hda'
- rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id( single_value[ 'id' ] ) ) )
+ if found_hdca:
+ raise ValueError("Only one collection may be supplied to parameter.")
+ if isinstance( single_value, dict ) and 'src' in single_value and 'id' in single_value:
+ if single_value['src'] == 'hda':
+ rval.append(trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(single_value['id']) ))
+ elif single_value['src'] == 'hdca':
+ found_hdca = True
+ decoded_id = trans.app.security.decode_id( single_value[ 'id' ] )
+ rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
+ else:
+ raise ValueError("Unknown input source %s passed to job submission API." % single_value['src'])
else:
rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( single_value ) )
elif isinstance( value, trans.app.model.HistoryDatasetAssociation ):
https://bitbucket.org/galaxy/galaxy-central/commits/7229b9c37193/
Changeset: 7229b9c37193
Branch: release_15.03
User: carlfeberhard
Date: 2015-03-02 19:22:00+00:00
Summary: Fix to remove validation of genome builds since some data source tools will assign invalid genome builds and later validation makes these hdas un-updatable
Affected #: 1 file
diff -r c0eef4e238198d40654404bc3baa2ec2e9565a1c -r 7229b9c37193b4b2ac3821cc77827e21dd9c1430 lib/galaxy/managers/base.py
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -789,10 +789,13 @@
# TODO: is this correct?
if val is None:
return '?'
- for genome_build_shortname, longname in self.app.genome_builds.get_genome_build_names( trans=trans ):
- if val == genome_build_shortname:
- return val
- raise exceptions.RequestParameterInvalidException( "invalid reference", key=key, val=val )
+ # currently, data source sites like UCSC are able to set the genome build to non-local build names
+ # afterwards, attempting to validate the whole model will choke here
+ # for genome_build_shortname, longname in self.app.genome_builds.get_genome_build_names( trans=trans ):
+ # if val == genome_build_shortname:
+ # return val
+ # raise exceptions.RequestParameterInvalidException( "invalid reference", key=key, val=val )
+ return val
# def slug( self, trans, item, key, val ):
# """validate slug"""
https://bitbucket.org/galaxy/galaxy-central/commits/c97672ccbe0d/
Changeset: c97672ccbe0d
Branch: release_15.03
User: dannon
Date: 2015-03-02 19:54:29+00:00
Summary: Rearranging the layers of middleware to allow sentry and debug to coexist without exploding (but you probably don't want to use both at once anyway)
Affected #: 1 file
diff -r 7229b9c37193b4b2ac3821cc77827e21dd9c1430 -r c97672ccbe0df0ff41ad750fe67bcaf91bae16d9 lib/galaxy/webapps/tool_shed/buildapp.py
--- a/lib/galaxy/webapps/tool_shed/buildapp.py
+++ b/lib/galaxy/webapps/tool_shed/buildapp.py
@@ -171,14 +171,6 @@
from paste import recursive
app = recursive.RecursiveMiddleware( app, conf )
log.debug( "Enabling 'recursive' middleware" )
- # If sentry logging is enabled, log here before propogating up to
- # the error middleware
- # TODO sentry config is duplicated between tool_shed/galaxy, refactor this.
- sentry_dsn = conf.get( 'sentry_dsn', None )
- if sentry_dsn:
- from galaxy.web.framework.middleware.sentry import Sentry
- log.debug( "Enabling 'sentry' middleware" )
- app = Sentry( app, sentry_dsn )
# Various debug middleware that can only be turned on if the debug
# flag is set, either because they are insecure or greatly hurt
# performance
@@ -218,6 +210,14 @@
from paste.translogger import TransLogger
app = TransLogger( app )
log.debug( "Enabling 'trans logger' middleware" )
+ # If sentry logging is enabled, log here before propogating up to
+ # the error middleware
+ # TODO sentry config is duplicated between tool_shed/galaxy, refactor this.
+ sentry_dsn = conf.get( 'sentry_dsn', None )
+ if sentry_dsn:
+ from galaxy.web.framework.middleware.sentry import Sentry
+ log.debug( "Enabling 'sentry' middleware" )
+ app = Sentry( app, sentry_dsn )
# X-Forwarded-Host handling
from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
app = XForwardedHostMiddleware( app )
https://bitbucket.org/galaxy/galaxy-central/commits/e32123bf153c/
Changeset: e32123bf153c
Branch: release_15.03
User: martenson
Date: 2015-03-02 21:33:43+00:00
Summary: tweak toolbox search to provide better (and more) results
with the inclusion of toolhelp in index and with more versions
of the same tools being massively installed the search results were
inconsistent and inaccurate and incomplete.
addresses https://trello.com/c/6Bvbduci/2486-toolbox-search-is-behaving-wrongly-diffe…
Affected #: 7 files
diff -r c97672ccbe0df0ff41ad750fe67bcaf91bae16d9 -r e32123bf153c01392df64601d7a093fb04ae339c client/galaxy/scripts/galaxy.workflows.js
--- a/client/galaxy/scripts/galaxy.workflows.js
+++ b/client/galaxy/scripts/galaxy.workflows.js
@@ -24,7 +24,7 @@
$(this).addClass("search_active");
// input.addClass(config.loadingClass);
// Add '*' to facilitate partial matching.
- var q = this.value + '*';
+ var q = this.value;
// Stop previous ajax-request
if (this.timer) {
clearTimeout(this.timer);
diff -r c97672ccbe0df0ff41ad750fe67bcaf91bae16d9 -r e32123bf153c01392df64601d7a093fb04ae339c client/galaxy/scripts/mvc/tools.js
--- a/client/galaxy/scripts/mvc/tools.js
+++ b/client/galaxy/scripts/mvc/tools.js
@@ -376,7 +376,7 @@
}
// Do search via AJAX.
- var q = query + '*';
+ var q = query;
// Stop previous ajax-request
if (this.timer) {
clearTimeout(this.timer);
diff -r c97672ccbe0df0ff41ad750fe67bcaf91bae16d9 -r e32123bf153c01392df64601d7a093fb04ae339c lib/galaxy/tools/search/__init__.py
--- a/lib/galaxy/tools/search/__init__.py
+++ b/lib/galaxy/tools/search/__init__.py
@@ -1,18 +1,27 @@
-from galaxy.eggs import require
+"""
+Module for building and searching the index of tools
+installed within this Galaxy.
+"""
+from galaxy import eggs
from galaxy.web.framework.helpers import to_unicode
-require( "Whoosh" )
+eggs.require( "Whoosh" )
from whoosh.filedb.filestore import RamStorage
from whoosh.fields import Schema, STORED, TEXT
from whoosh.scoring import BM25F
from whoosh.qparser import MultifieldParser
-schema = Schema( id=STORED, title=TEXT, description=TEXT, help=TEXT )
-
+schema = Schema( id=STORED,
+ title=TEXT,
+ description=TEXT,
+ section=TEXT,
+ help=TEXT )
+import logging
+log = logging.getLogger( __name__ )
class ToolBoxSearch( object ):
"""
Support searching tools in a toolbox. This implementation uses
- the "whoosh" search library.
+ the Whoosh search library.
"""
def __init__( self, toolbox, index_help=True ):
@@ -26,13 +35,13 @@
self.storage = RamStorage()
self.index = self.storage.create_index( schema )
writer = self.index.writer()
- ## TODO: would also be nice to search section headers.
for id, tool in self.toolbox.tools():
add_doc_kwds = {
"id": id,
- "title": to_unicode(tool.name),
- "description": to_unicode(tool.description),
- "help": to_unicode(""),
+ "title": to_unicode( tool.name ),
+ "description": to_unicode( tool.description ),
+ "section": to_unicode( tool.get_panel_section()[1] if len( tool.get_panel_section() ) == 2 else '' ),
+ "help": to_unicode( "" ),
}
if index_help and tool.help:
try:
@@ -45,13 +54,18 @@
writer.commit()
def search( self, query, return_attribute='id' ):
- # Change field boosts for searcher to place more weight on title, description than help.
+ # Change field boosts for searcher
searcher = self.index.searcher(
weighting=BM25F(
- field_B={ 'title_B': 3, 'description_B': 2, 'help_B': 1 }
+ field_B={ 'title_B': 9,
+ 'section_B': 3,
+ 'description_B': 2,
+ 'help_B': 0.5 }
)
)
- # Set query to search title, description, and help.
- parser = MultifieldParser( [ 'title', 'description', 'help' ], schema=schema )
- results = searcher.search( parser.parse( query ) )
- return [ result[ return_attribute ] for result in results ]
+ # Set query to search title, description, section, and help.
+ parser = MultifieldParser( [ 'title', 'description', 'section', 'help' ], schema=schema )
+ # Perform the search
+ hits = searcher.search( parser.parse( '*' + query + '*' ), limit=20 )
+
+ return [ hit[ return_attribute ] for hit in hits ]
diff -r c97672ccbe0df0ff41ad750fe67bcaf91bae16d9 -r e32123bf153c01392df64601d7a093fb04ae339c static/scripts/galaxy.workflows.js
--- a/static/scripts/galaxy.workflows.js
+++ b/static/scripts/galaxy.workflows.js
@@ -24,7 +24,7 @@
$(this).addClass("search_active");
// input.addClass(config.loadingClass);
// Add '*' to facilitate partial matching.
- var q = this.value + '*';
+ var q = this.value;
// Stop previous ajax-request
if (this.timer) {
clearTimeout(this.timer);
diff -r c97672ccbe0df0ff41ad750fe67bcaf91bae16d9 -r e32123bf153c01392df64601d7a093fb04ae339c static/scripts/mvc/tools.js
--- a/static/scripts/mvc/tools.js
+++ b/static/scripts/mvc/tools.js
@@ -376,7 +376,7 @@
}
// Do search via AJAX.
- var q = query + '*';
+ var q = query;
// Stop previous ajax-request
if (this.timer) {
clearTimeout(this.timer);
diff -r c97672ccbe0df0ff41ad750fe67bcaf91bae16d9 -r e32123bf153c01392df64601d7a093fb04ae339c static/scripts/packed/galaxy.workflows.js
--- a/static/scripts/packed/galaxy.workflows.js
+++ b/static/scripts/packed/galaxy.workflows.js
@@ -1,1 +1,1 @@
-$(function(){if(window.lt_ie_7){show_modal("Browser not supported","Sorry, the workflow editor is not supported for IE6 and below.");return}$("#tool-search-query").click(function(){$(this).focus();$(this).select()}).keyup(function(){$(this).css("font-style","normal");if(this.value.length<3){reset_tool_search(false)}else{if(this.value!=this.lastValue){$(this).addClass("search_active");var g=this.value+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();this.timer=setTimeout(function(){$.get(tool_search_url,{query:g},function(i){$("#search-no-results").hide();$(".toolSectionWrapper").hide();$(".toolSectionWrapper").find(".toolTitle").hide();if(i.length!=0){var h=$.map(i,function(k,j){return"link-"+k});$(h).each(function(j,k){$("[id='"+k+"']").parent().addClass("search_match");$("[id='"+k+"']").parent().show().parent().parent().show().parent().show()});$(".toolPanelLabel").each(function(){var l=$(this);var k=l.next();var j=true;while(k.length!==0&&k.hasClass("toolTitle")){if(k.is(":visible")){j=false;break}else{k=k.next()}}if(j){l.hide()}})}else{$("#search-no-results").show()}$("#search-spinner").hide()},"json")},200)}}this.lastValue=this.value});canvas_manager=new CanvasManager($("#canvas-viewport"),$("#overview"));reset();$.ajax({url:get_datatypes_url,dataType:"json",cache:false,success:function(g){populate_datatype_info(g);$.ajax({url:load_workflow_url,data:{id:workflow_id,_:"true"},dataType:"json",cache:false,success:function(h){reset();workflow.from_simple(h);workflow.has_changes=false;workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview();upgrade_message="";$.each(h.upgrade_messages,function(j,i){upgrade_message+=("<li>Step "+(parseInt(j,10)+1)+": "+workflow.nodes[j].name+"<ul>");$.each(i,function(k,l){upgrade_message+="<li>"+l+"</li>"});upgrade_message+="</ul></li>"});if(upgrade_message){show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal})}else{hide_modal()}show_workflow_parameters()},beforeSubmit:function(h){show_message("Loading workflow","progress")}})}});$(document).ajaxStart(function(){active_ajax_call=true;$(document).bind("ajaxStop.global",function(){active_ajax_call=false})});$(document).ajaxError(function(i,g){var h=g.responseText||g.statusText||"Could not connect to server";show_modal("Server error",h,{"Ignore error":hide_modal});return false});make_popupmenu($("#workflow-options-button"),{Save:save_current_workflow,Run:function(){window.location=run_workflow_url},"Edit Attributes":c,"Auto Re-layout":f,Close:close_editor});function b(){workflow.clear_active_node();$(".right-content").hide();var j="";for(var h in workflow.nodes){var i=workflow.nodes[h];if(i.type=="tool"){j+="<div class='toolForm' style='margin-bottom:5px;'><div class='toolFormTitle'>Step "+i.id+" - "+i.name+"</div>";for(var k in i.output_terminals){var g=i.output_terminals[k];if($.inArray(g.name,i.workflow_outputs)!=-1){j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' checked /></p>"}else{j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' /></p>"}}j+="</div>"}}$("#output-fill-area").html(j);$("#output-fill-area input").bind("click",function(){var n=this.name.split("|")[0];var l=this.name.split("|")[1];if(this.checked){if($.inArray(l,workflow.nodes[n].workflow_outputs)==-1){workflow.nodes[n].workflow_outputs.push(l)}}else{while($.inArray(l,workflow.nodes[n].workflow_outputs)!=-1){var m=$.inArray(l,workflow.nodes[n].workflow_outputs);workflow.nodes[n].workflow_outputs=workflow.nodes[n].workflow_outputs.slice(0,m).concat(workflow.nodes[n].workflow_outputs.slice(m+1))}}workflow.has_changes=true});$("#workflow-output-area").show()}function f(){workflow.layout();workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview()}function c(){workflow.clear_active_node();$(".right-content").hide();$("#edit-attributes").show()}overview_size=$.jStorage.get("overview-size");if(overview_size!==undefined){$("#overview-border").css({width:overview_size,height:overview_size})}if($.jStorage.get("overview-off")){d()}else{e()}$("#overview-border").bind("dragend",function(h,j){var k=$(this).offsetParent();var i=k.offset();var g=Math.max(k.width()-(j.offsetX-i.left),k.height()-(j.offsetY-i.top));$.jStorage.set("overview-size",g+"px")});function e(){$.jStorage.set("overview-off",false);$("#overview-border").css("right","0px");$("#close-viewport").css("background-position","0px 0px")}function d(){$.jStorage.set("overview-off",true);$("#overview-border").css("right","20000px");$("#close-viewport").css("background-position","12px 0px")}$("#close-viewport").click(function(){if($("#overview-border").css("right")==="0px"){d()}else{e()}});window.onbeforeunload=function(){if(workflow&&workflow.has_changes){return"There are unsaved changes to your workflow which will be lost."}};$("div.toolSectionBody").hide();$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var a=null;$("div.toolSectionTitle").each(function(){var g=$(this).next("div.toolSectionBody");$(this).click(function(){if(g.is(":hidden")){if(a){a.slideUp("fast")}a=g;g.slideDown("fast")}else{g.slideUp("fast");a=null}})});async_save_text("workflow-name","workflow-name",rename_async_url,"new_name");$("#workflow-tag").click(function(){$(".tag-area").click();return false});async_save_text("workflow-annotation","workflow-annotation",annotate_async_url,"new_annotation",25,true,4)});function reset(){if(workflow){workflow.remove_all()}workflow=new Workflow($("#canvas-container"))}function scroll_to_nodes(){var a=$("#canvas-viewport");var d=$("#canvas-container");var c,b;if(d.width()<a.width()){b=(a.width()-d.width())/2}else{b=0}if(d.height()<a.height()){c=(a.height()-d.height())/2}else{c=0}d.css({left:b,top:c})}function add_node_for_tool(b,a){node=add_node("tool",a,b);$.ajax({url:get_new_module_info_url,data:{type:"tool",tool_id:b,_:"true"},global:false,dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status===0){c+=", server unavailable"}node.error(c)}})}function add_node_for_module(a,b){node=add_node(a,b);$.ajax({url:get_new_module_info_url,data:{type:a,_:"true"},dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status==0){c+=", server unavailable"}node.error(c)}})}function display_pja(b,a){$("#pja_container").append(get_pja_form(b,a));$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text();$(this).closest(".toolForm").remove();delete workflow.active_node.post_job_actions[action_to_rem];workflow.active_form_has_changes=true})}function display_pja_list(){return pja_list}function display_file_list(b){addlist="<select id='node_data_list' name='node_data_list'>";for(var a in b.output_terminals){addlist+="<option value='"+a+"'>"+a+"</option>"}addlist+="</select>";return addlist}function new_pja(d,b,a){if(a.post_job_actions===undefined){a.post_job_actions={}}if(a.post_job_actions[d+b]===undefined){var c={};c.action_type=d;c.output_name=b;a.post_job_actions[d+b]=null;a.post_job_actions[d+b]=c;display_pja(c,a);workflow.active_form_has_changes=true;return true}else{return false}}function show_workflow_parameters(){var c=/\$\{.+?\}/g;var b=[];var f=$("#workflow-parameters-container");var e=$("#workflow-parameters-box");var a="";var d=[];$.each(workflow.nodes,function(g,h){var i=h.form_html.match(c);if(i){d=d.concat(i)}if(h.post_job_actions){$.each(h.post_job_actions,function(j,l){if(l.action_arguments){$.each(l.action_arguments,function(m,n){var 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d=this;$(this).find("select[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find("input[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find(".popupmenu").each(function(){var g=$(this).parents("div.form-row").attr("id");var e=$('<a class="popup-arrow" id="popup-arrow-for-'+g+'">▼</a>');var f={};$(this).find("button").each(function(){var h=$(this).attr("name");var i=$(this).attr("value");f[$(this).text()]=function(){$(d).append("<input type='hidden' name='"+h+"' value='"+i+"' />").submit()}});e.insertAfter(this);$(this).remove();make_popupmenu(e,f)});$(this).find("input,textarea,select").each(function(){$(this).bind("focus click",function(){workflow.active_form_has_changes=true})})})}var close_editor=function(){workflow.check_changes_in_active_form();if(workflow&&workflow.has_changes){do_close=function(){window.onbeforeunload=undefined;window.document.location=workflow_index_url};show_modal("Close workflow editor","There are unsaved changes to 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\ No newline at end of file
+$(function(){if(window.lt_ie_7){show_modal("Browser not supported","Sorry, the workflow editor is not supported for IE6 and below.");return}$("#tool-search-query").click(function(){$(this).focus();$(this).select()}).keyup(function(){$(this).css("font-style","normal");if(this.value.length<3){reset_tool_search(false)}else{if(this.value!=this.lastValue){$(this).addClass("search_active");var g=this.value;if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();this.timer=setTimeout(function(){$.get(tool_search_url,{query:g},function(i){$("#search-no-results").hide();$(".toolSectionWrapper").hide();$(".toolSectionWrapper").find(".toolTitle").hide();if(i.length!=0){var h=$.map(i,function(k,j){return"link-"+k});$(h).each(function(j,k){$("[id='"+k+"']").parent().addClass("search_match");$("[id='"+k+"']").parent().show().parent().parent().show().parent().show()});$(".toolPanelLabel").each(function(){var l=$(this);var k=l.next();var j=true;while(k.length!==0&&k.hasClass("toolTitle")){if(k.is(":visible")){j=false;break}else{k=k.next()}}if(j){l.hide()}})}else{$("#search-no-results").show()}$("#search-spinner").hide()},"json")},200)}}this.lastValue=this.value});canvas_manager=new CanvasManager($("#canvas-viewport"),$("#overview"));reset();$.ajax({url:get_datatypes_url,dataType:"json",cache:false,success:function(g){populate_datatype_info(g);$.ajax({url:load_workflow_url,data:{id:workflow_id,_:"true"},dataType:"json",cache:false,success:function(h){reset();workflow.from_simple(h);workflow.has_changes=false;workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview();upgrade_message="";$.each(h.upgrade_messages,function(j,i){upgrade_message+=("<li>Step "+(parseInt(j,10)+1)+": "+workflow.nodes[j].name+"<ul>");$.each(i,function(k,l){upgrade_message+="<li>"+l+"</li>"});upgrade_message+="</ul></li>"});if(upgrade_message){show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). 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i.output_terminals){var g=i.output_terminals[k];if($.inArray(g.name,i.workflow_outputs)!=-1){j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' checked /></p>"}else{j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' /></p>"}}j+="</div>"}}$("#output-fill-area").html(j);$("#output-fill-area input").bind("click",function(){var n=this.name.split("|")[0];var l=this.name.split("|")[1];if(this.checked){if($.inArray(l,workflow.nodes[n].workflow_outputs)==-1){workflow.nodes[n].workflow_outputs.push(l)}}else{while($.inArray(l,workflow.nodes[n].workflow_outputs)!=-1){var m=$.inArray(l,workflow.nodes[n].workflow_outputs);workflow.nodes[n].workflow_outputs=workflow.nodes[n].workflow_outputs.slice(0,m).concat(workflow.nodes[n].workflow_outputs.slice(m+1))}}workflow.has_changes=true});$("#workflow-output-area").show()}function f(){workflow.layout();workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview()}function c(){workflow.clear_active_node();$(".right-content").hide();$("#edit-attributes").show()}overview_size=$.jStorage.get("overview-size");if(overview_size!==undefined){$("#overview-border").css({width:overview_size,height:overview_size})}if($.jStorage.get("overview-off")){d()}else{e()}$("#overview-border").bind("dragend",function(h,j){var k=$(this).offsetParent();var i=k.offset();var g=Math.max(k.width()-(j.offsetX-i.left),k.height()-(j.offsetY-i.top));$.jStorage.set("overview-size",g+"px")});function e(){$.jStorage.set("overview-off",false);$("#overview-border").css("right","0px");$("#close-viewport").css("background-position","0px 0px")}function d(){$.jStorage.set("overview-off",true);$("#overview-border").css("right","20000px");$("#close-viewport").css("background-position","12px 0px")}$("#close-viewport").click(function(){if($("#overview-border").css("right")==="0px"){d()}else{e()}});window.onbeforeunload=function(){if(workflow&&workflow.has_changes){return"There are unsaved changes 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\ No newline at end of file
diff -r c97672ccbe0df0ff41ad750fe67bcaf91bae16d9 -r e32123bf153c01392df64601d7a093fb04ae339c static/scripts/packed/mvc/tools.js
--- a/static/scripts/packed/mvc/tools.js
+++ b/static/scripts/packed/mvc/tools.js
@@ -1,1 +1,1 @@
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l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){y.each(this.attributes.elems,function(A){A.show()});this.show();this.set("open",false)},apply_search_results:function(B){var C=true,A;y.each(this.attributes.elems,function(D){if(D instanceof w){A=D;A.hide()}else{if(D instanceof j){if(D.apply_search_results(B)){C=false;if(A){A.show()}}}}});if(C){this.hide()}else{this.show();this.set("open",true)}}});y.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var C=this.attributes.query;if(C.length<this.attributes.min_chars_for_search){this.set("results",null);return}var B=C+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var A=this;this.timer=setTimeout(function(){$.get(A.attributes.search_url,{query:B},function(D){A.set("results",D);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});y.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(A){this.attributes.tool_search=A.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=A.tools;this.attributes.layout=new Backbone.Collection(this.parse(A.layout))},parse:function(B){var A=this,C=function(F){var E=F.model_class;if(E.indexOf("Tool")===E.length-4){return A.attributes.tools.get(F.id)}else{if(E==="ToolSection"){var D=y.map(F.elems,C);F.elems=D;return new l(F)}else{if(E==="ToolSectionLabel"){return new w(F)}}}};return y.map(B,C)},clear_search_results:function(){this.get("layout").each(function(A){if(A instanceof l){A.clear_search_results()}else{A.show()}})},apply_search_results:function(){var B=this.get("tool_search").get("results");if(B===null){this.clear_search_results();return}var A=null;this.get("layout").each(function(C){if(C instanceof w){A=C;A.hide()}else{if(C instanceof j){if(C.apply_search_results(B)){if(A){A.show()}}}else{A=null;C.apply_search_results(B)}}})}});var t=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=t.extend({tagName:"div",render:function(){var A=$("<div/>");A.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){A.find("a").on("click",function(B){B.preventDefault();Galaxy.upload.show()})}this.$el.append(A);return this}});var b=t.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=t.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){t.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var A=this.$el.find(".toolSectionBody");y.each(this.model.attributes.elems,function(B){if(B instanceof j){var C=new m({model:B,className:"toolTitle"});C.render();A.append(C.$el)}else{if(B instanceof w){var D=new b({model:B});D.render();A.append(D.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(A){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===A.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var x=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var A=this;var B=new p({model:this.model.get("tool_search")});B.render();A.$el.append(B.$el);this.model.get("layout").each(function(D){if(D instanceof l){var C=new r({model:D});C.render();A.$el.append(C.$el)}else{if(D instanceof j){var E=new m({model:D,className:"toolTitleNoSection"});E.render();A.$el.append(E.$el)}else{if(D instanceof w){var F=new b({model:D});F.render();A.$el.append(F.$el)}}}});A.$el.find("a.tool-link").click(function(E){var D=$(this).attr("class").split(/\s+/)[0],C=A.model.get("tools").get(D);A.trigger("tool_link_click",E,C)});return this},handle_search_results:function(){var A=this.model.get("tool_search").get("results");if(A&&A.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var v=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new x({collection:this.collection});this.tool_form_view=new v()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var A=this;this.tool_panel_view.on("tool_link_click",function(C,B){C.preventDefault();A.show_tool(B)})},show_tool:function(B){var A=this;B.fetch().done(function(){A.tool_form_view.model=B;A.tool_form_view.render();A.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:u,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:x,ToolFormView:v}});
\ No newline at end of file
+define(["libs/underscore","viz/trackster/util","mvc/data","libs/lunr"],function(y,a,z,s){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(A){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(A){this.set("value",A||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(A){this.set("value",parseInt(A,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(A){this.set("value",parseFloat(A))}});var u=e.extend({get_samples:function(){return y.map(this.get("options"),function(A){return A[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:u};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(A){this.set("inputs",new i(y.map(A.inputs,function(B){var C=e.subModelTypes[B.type]||e;return new C(B)})))},toJSON:function(){var A=Backbone.Model.prototype.toJSON.call(this);A.inputs=this.get("inputs").map(function(B){return B.toJSON()});return A},remove_inputs:function(B){var A=this,C=A.get("inputs").filter(function(D){return(B.indexOf(D.get("type"))!==-1)});A.get("inputs").remove(C)},copy:function(B){var C=new j(this.toJSON());if(B){var A=new Backbone.Collection();C.get("inputs").each(function(D){if(D.get_samples()){A.push(D)}});C.set("inputs",A)}return C},apply_search_results:function(A){(y.indexOf(A,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(A,B){this.get("inputs").find(function(C){return C.get("name")===A}).set("value",B)},set_input_values:function(B){var A=this;y.each(y.keys(B),function(C){A.set_input_value(C,B[C])})},run:function(){return this._run()},rerun:function(B,A){return this._run({action:"rerun",target_dataset_id:B.id,regions:A})},get_inputs_dict:function(){var A={};this.get("inputs").each(function(B){A[B.get("name")]=B.get("value")});return A},_run:function(C){var D=y.extend({tool_id:this.id,inputs:this.get_inputs_dict()},C);var B=$.Deferred(),A=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(D),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(E){return E!=="pending"}});$.when(A.go()).then(function(E){B.resolve(new z.DatasetCollection().reset(E))});return B}});y.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var w=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){y.each(this.attributes.elems,function(A){A.show()});this.show();this.set("open",false)},apply_search_results:function(B){var C=true,A;y.each(this.attributes.elems,function(D){if(D instanceof w){A=D;A.hide()}else{if(D instanceof j){if(D.apply_search_results(B)){C=false;if(A){A.show()}}}}});if(C){this.hide()}else{this.show();this.set("open",true)}}});y.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var C=this.attributes.query;if(C.length<this.attributes.min_chars_for_search){this.set("results",null);return}var B=C;if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var A=this;this.timer=setTimeout(function(){$.get(A.attributes.search_url,{query:B},function(D){A.set("results",D);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});y.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(A){this.attributes.tool_search=A.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=A.tools;this.attributes.layout=new Backbone.Collection(this.parse(A.layout))},parse:function(B){var A=this,C=function(F){var E=F.model_class;if(E.indexOf("Tool")===E.length-4){return A.attributes.tools.get(F.id)}else{if(E==="ToolSection"){var D=y.map(F.elems,C);F.elems=D;return new l(F)}else{if(E==="ToolSectionLabel"){return new w(F)}}}};return y.map(B,C)},clear_search_results:function(){this.get("layout").each(function(A){if(A instanceof l){A.clear_search_results()}else{A.show()}})},apply_search_results:function(){var B=this.get("tool_search").get("results");if(B===null){this.clear_search_results();return}var A=null;this.get("layout").each(function(C){if(C instanceof w){A=C;A.hide()}else{if(C instanceof j){if(C.apply_search_results(B)){if(A){A.show()}}}else{A=null;C.apply_search_results(B)}}})}});var t=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=t.extend({tagName:"div",render:function(){var A=$("<div/>");A.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){A.find("a").on("click",function(B){B.preventDefault();Galaxy.upload.show()})}this.$el.append(A);return this}});var b=t.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=t.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){t.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var A=this.$el.find(".toolSectionBody");y.each(this.model.attributes.elems,function(B){if(B instanceof j){var C=new m({model:B,className:"toolTitle"});C.render();A.append(C.$el)}else{if(B instanceof w){var D=new b({model:B});D.render();A.append(D.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(A){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===A.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var x=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var A=this;var B=new p({model:this.model.get("tool_search")});B.render();A.$el.append(B.$el);this.model.get("layout").each(function(D){if(D instanceof l){var C=new r({model:D});C.render();A.$el.append(C.$el)}else{if(D instanceof j){var E=new m({model:D,className:"toolTitleNoSection"});E.render();A.$el.append(E.$el)}else{if(D instanceof w){var F=new b({model:D});F.render();A.$el.append(F.$el)}}}});A.$el.find("a.tool-link").click(function(E){var D=$(this).attr("class").split(/\s+/)[0],C=A.model.get("tools").get(D);A.trigger("tool_link_click",E,C)});return this},handle_search_results:function(){var A=this.model.get("tool_search").get("results");if(A&&A.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var v=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new x({collection:this.collection});this.tool_form_view=new v()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var A=this;this.tool_panel_view.on("tool_link_click",function(C,B){C.preventDefault();A.show_tool(B)})},show_tool:function(B){var A=this;B.fetch().done(function(){A.tool_form_view.model=B;A.tool_form_view.render();A.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:u,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:x,ToolFormView:v}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/2a96f18494a3/
Changeset: 2a96f18494a3
Branch: release_15.03
User: guerler
Date: 2015-03-02 23:12:34+00:00
Summary: Parameters: Cover additional case for multiple hdas
Affected #: 1 file
diff -r e32123bf153c01392df64601d7a093fb04ae339c -r 2a96f18494a39585d33f23e7286aa3dc6bbaeeb0 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2000,6 +2000,8 @@
rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
else:
raise ValueError("Unknown input source %s passed to job submission API." % single_value['src'])
+ elif isinstance( single_value, trans.app.model.HistoryDatasetAssociation ):
+ rval.append( single_value )
else:
rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( single_value ) )
elif isinstance( value, trans.app.model.HistoryDatasetAssociation ):
https://bitbucket.org/galaxy/galaxy-central/commits/0b397892660a/
Changeset: 0b397892660a
Branch: release_15.03
User: guerler
Date: 2015-03-02 23:25:46+00:00
Summary: Parameters: Fix collection selection for multiple dataset input field
Affected #: 5 files
diff -r 2a96f18494a39585d33f23e7286aa3dc6bbaeeb0 -r 0b397892660afd13f845b6ea9d03634158f8fb9d client/galaxy/scripts/mvc/tools/tools-select-content.js
--- a/client/galaxy/scripts/mvc/tools/tools-select-content.js
+++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js
@@ -217,7 +217,7 @@
}
// identify suitable select field
- if (new_value && new_value.values.length > 0 && new_value.values[0].src == 'hcda') {
+ if (new_value && new_value.values.length > 0 && new_value.values[0].src == 'hdca') {
this.current = 'collection';
this.select_collection.value(list[0]);
} else {
diff -r 2a96f18494a39585d33f23e7286aa3dc6bbaeeb0 -r 0b397892660afd13f845b6ea9d03634158f8fb9d lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2316,6 +2316,11 @@
'id' : trans.security.encode_id(v.id),
'src' : 'hda'
}
+ elif isinstance(v, trans.app.model.HistoryDatasetCollectionAssociation):
+ return {
+ 'id' : trans.security.encode_id(v.id),
+ 'src' : 'hdca'
+ }
elif isinstance(v, bool):
if v is True:
return 'true'
diff -r 2a96f18494a39585d33f23e7286aa3dc6bbaeeb0 -r 0b397892660afd13f845b6ea9d03634158f8fb9d lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2018,6 +2018,8 @@
encoded_id = str( value )[ len( "__collection_reduce__|" ): ]
decoded_id = trans.app.security.decode_id( encoded_id )
rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
+ elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ):
+ rval = value
else:
rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value )
if isinstance( rval, list ):
diff -r 2a96f18494a39585d33f23e7286aa3dc6bbaeeb0 -r 0b397892660afd13f845b6ea9d03634158f8fb9d static/scripts/mvc/tools/tools-select-content.js
--- a/static/scripts/mvc/tools/tools-select-content.js
+++ b/static/scripts/mvc/tools/tools-select-content.js
@@ -217,7 +217,7 @@
}
// identify suitable select field
- if (new_value && new_value.values.length > 0 && new_value.values[0].src == 'hcda') {
+ if (new_value && new_value.values.length > 0 && new_value.values[0].src == 'hdca') {
this.current = 'collection';
this.select_collection.value(list[0]);
} else {
diff -r 2a96f18494a39585d33f23e7286aa3dc6bbaeeb0 -r 0b397892660afd13f845b6ea9d03634158f8fb9d static/scripts/packed/mvc/tools/tools-select-content.js
--- a/static/scripts/packed/mvc/tools/tools-select-content.js
+++ b/static/scripts/packed/mvc/tools/tools-select-content.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hdca"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/93cd3e9ca4be/
Changeset: 93cd3e9ca4be
Branch: release_15.03
User: jmchilton
Date: 2015-03-03 02:32:30+00:00
Summary: Tool data API testing fixes.
- Add files I didn't commit previously in test/functional/tool-data/.
- Comment out test for tool data table deletion since Dan fixed the problem of regular users running data managers through the API (https://github.com/galaxyproject/galaxy/commit/48f77dc742acf01ddbafafcc4634…) that I previously exploited to write the test.
Affected #: 5 files
diff -r 0b397892660afd13f845b6ea9d03634158f8fb9d -r 93cd3e9ca4be80dadfe92f7ffc0e6d11283c34fc test/api/test_tool_data.py
--- a/test/api/test_tool_data.py
+++ b/test/api/test_tool_data.py
@@ -1,11 +1,6 @@
""" Tests for the tool data API.
"""
-import json
-
from base import api
-from .helpers import DatasetPopulator
-
-from requests import delete
import operator
@@ -40,7 +35,7 @@
field = show_field_response.json()
self._assert_has_keys( field, "files", "name", "fields", "fingerprint", "base_dir" )
files = field[ "files" ]
- assert len( files ) == 2
+ assert len( files ) == 2, "Length of files [%s] was not 2." % files
def test_download_field_file(self):
show_field_response = self._get( "tool_data/testalpha/fields/data1/files/entry.txt", admin=True )
@@ -48,27 +43,32 @@
content = show_field_response.content
assert content == "This is data 1.", content
- def test_delete_entry(self):
- show_response = self._get( "tool_data/testbeta", admin=True )
- original_count = len(show_response.json()["fields"])
+ # Following test case rendered invalid by the fix in
+ # https://github.com/galaxyproject/galaxy/commit/48f77dc742acf01ddbafafcc4634….
+ # TODO: Restore the test case when test framework allows actions from
+ # admin users.
- dataset_populator = DatasetPopulator( self.galaxy_interactor )
- history_id = dataset_populator.new_history()
- payload = dataset_populator.run_tool_payload(
- tool_id="data_manager",
- inputs={"ignored_value": "moo"},
- history_id=history_id,
- )
- create_response = self._post( "tools", data=payload )
- self._assert_status_code_is( create_response, 200 )
- dataset_populator.wait_for_history( history_id, assert_ok=True )
- show_response = self._get( "tool_data/testbeta", admin=True )
- updated_fields = show_response.json()["fields"]
- assert len(updated_fields) == original_count + 1
- field0 = updated_fields[0]
- url = self._api_url( "tool_data/testbeta?key=%s" % self.galaxy_interactor.master_api_key )
- delete( url, data=json.dumps({"values": "\t".join(field0)}) )
+ # def test_delete_entry(self):
+ # show_response = self._get( "tool_data/testbeta", admin=True )
+ # original_count = len(show_response.json()["fields"])
- show_response = self._get( "tool_data/testbeta", admin=True )
- updated_fields = show_response.json()["fields"]
- assert len(updated_fields) == original_count
+ # dataset_populator = DatasetPopulator( self.galaxy_interactor )
+ # history_id = dataset_populator.new_history()
+ # payload = dataset_populator.run_tool_payload(
+ # tool_id="data_manager",
+ # inputs={"ignored_value": "moo"},
+ # history_id=history_id,
+ # )
+ # create_response = self._post( "tools", data=payload )
+ # self._assert_status_code_is( create_response, 200 )
+ # dataset_populator.wait_for_history( history_id, assert_ok=True )
+ # show_response = self._get( "tool_data/testbeta", admin=True )
+ # updated_fields = show_response.json()["fields"]
+ # assert len(updated_fields) == original_count + 1
+ # field0 = updated_fields[0]
+ # url = self._api_url( "tool_data/testbeta?key=%s" % self.galaxy_interactor.master_api_key )
+ # delete( url, data=json.dumps({"values": "\t".join(field0)}) )
+
+ # show_response = self._get( "tool_data/testbeta", admin=True )
+ # updated_fields = show_response.json()["fields"]
+ # assert len(updated_fields) == original_count
diff -r 0b397892660afd13f845b6ea9d03634158f8fb9d -r 93cd3e9ca4be80dadfe92f7ffc0e6d11283c34fc test/functional/tool-data/data1/entry.txt
--- /dev/null
+++ b/test/functional/tool-data/data1/entry.txt
@@ -0,0 +1,1 @@
+This is data 1.
\ No newline at end of file
diff -r 0b397892660afd13f845b6ea9d03634158f8fb9d -r 93cd3e9ca4be80dadfe92f7ffc0e6d11283c34fc test/functional/tool-data/data1/entry.txt.index
--- /dev/null
+++ b/test/functional/tool-data/data1/entry.txt.index
@@ -0,0 +1,1 @@
+fancy compressed map built with cool algorithms...
\ No newline at end of file
diff -r 0b397892660afd13f845b6ea9d03634158f8fb9d -r 93cd3e9ca4be80dadfe92f7ffc0e6d11283c34fc test/functional/tool-data/data2/entry.txt
--- /dev/null
+++ b/test/functional/tool-data/data2/entry.txt
@@ -0,0 +1,1 @@
+This is data 2.
\ No newline at end of file
diff -r 0b397892660afd13f845b6ea9d03634158f8fb9d -r 93cd3e9ca4be80dadfe92f7ffc0e6d11283c34fc test/functional/tool-data/data2/entry.txt.index
--- /dev/null
+++ b/test/functional/tool-data/data2/entry.txt.index
@@ -0,0 +1,1 @@
+fancy compressed map built with cool algorithms...2
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/fb55f46bdd89/
Changeset: fb55f46bdd89
Branch: release_15.03
User: jmchilton
Date: 2015-03-03 03:31:32+00:00
Summary: Attempt to fix intermittently failing jobs API test.
Retry check several times in case there is some sort of timing problem where a history turns okay - before a job. Improve assertion error message.
Affected #: 1 file
diff -r 93cd3e9ca4be80dadfe92f7ffc0e6d11283c34fc -r fb55f46bdd89a01c7febdcb46cfe81923213e073 test/api/test_jobs.py
--- a/test/api/test_jobs.py
+++ b/test/api/test_jobs.py
@@ -29,14 +29,23 @@
def test_index_state_filter( self ):
# Initial number of ok jobs
original_count = len( self.__uploads_with_state( "ok" ) )
-
# Run through dataset upload to ensure num uplaods at least greater
# by 1.
self.__history_with_ok_dataset()
# Verify number of ok jobs is actually greater.
- new_count = len( self.__uploads_with_state( "ok" ) )
- assert original_count < new_count
+ count_increased = False
+ for i in range(10):
+ new_count = len( self.__uploads_with_state( "ok" ) )
+ if original_count < new_count:
+ count_increased = True
+ break
+ time.sleep(.1)
+
+ if not count_increased:
+ template = "Jobs in ok state did not increase (was %d, now %d)"
+ message = template % (original_count, new_count)
+ raise AssertionError(message)
def test_index_date_filter( self ):
self.__history_with_new_dataset()
https://bitbucket.org/galaxy/galaxy-central/commits/868bc05b413c/
Changeset: 868bc05b413c
Branch: release_15.03
User: jmchilton
Date: 2015-03-03 03:33:07+00:00
Summary: Clarify failing test test_tools.py.
Affected #: 1 file
diff -r fb55f46bdd89a01c7febdcb46cfe81923213e073 -r 868bc05b413c68f8589f68a525918cb8df463639 test/api/test_tools.py
--- a/test/api/test_tools.py
+++ b/test/api/test_tools.py
@@ -219,8 +219,9 @@
'col': "' ; echo 'moo",
}
response = self._run( "column_param", history_id, inputs )
- # TODO: make this test pass...
- self._assert_status_code_is( response, 400 )
+ if response.status_code == 200:
+ message = "Known, high priority issue. Column parameters are sanitized but invalid values should prevent execution and doesn't."
+ raise AssertionError(message)
@skip_without_tool( "collection_paired_test" )
def test_collection_parameter( self ):
https://bitbucket.org/galaxy/galaxy-central/commits/f276d935403a/
Changeset: f276d935403a
Branch: release_15.03
User: jmchilton
Date: 2015-03-03 03:34:40+00:00
Summary: Remove assert False from test/api/test_workflows_from_yaml.py.
These aren't ideal tests - but it is some indication that things are working that the API will import the workflow and produce a representation. Should follow up at some point and verify the representation is in fact the correct one.
Affected #: 1 file
diff -r 868bc05b413c68f8589f68a525918cb8df463639 -r f276d935403af57bdc3777a7b88550ce6d57d6de test/api/test_workflows_from_yaml.py
--- a/test/api/test_workflows_from_yaml.py
+++ b/test/api/test_workflows_from_yaml.py
@@ -100,8 +100,6 @@
$link: the_pause
""")
print self._get("workflows/%s/download" % workflow_id).json()
- assert False
- # TODO: fill out test...
def test_implicit_connections( self ):
workflow_id = self._upload_yaml_workflow("""
@@ -132,4 +130,3 @@
""")
workflow = self._get("workflows/%s/download" % workflow_id).json()
print workflow
- assert False
https://bitbucket.org/galaxy/galaxy-central/commits/814efb393019/
Changeset: 814efb393019
Branch: release_15.03
User: jmchilton
Date: 2015-03-03 14:30:55+00:00
Summary: Fix intermittently failing test test_workflow_run_dynamic_output_collections.
Love it when the bugs correspond to actual TODOs I left in the code.
Affected #: 1 file
diff -r f276d935403af57bdc3777a7b88550ce6d57d6de -r 814efb393019bec46ec9ac567d72d835210a982c test/api/test_workflows.py
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -570,11 +570,13 @@
'0': self._ds_entry(hda1),
'1': self._ds_entry(hda2),
}
- self.__invoke_workflow( history_id, workflow_id, inputs )
- # TODO: wait on workflow invocations
- time.sleep(10)
- self.dataset_populator.wait_for_history( history_id, assert_ok=True )
- self.assertEquals("10.0\n30.0\n20.0\n40.0\n", self.dataset_populator.get_history_dataset_content( history_id, hid=0 ) )
+ invocation_id = self.__invoke_workflow( history_id, workflow_id, inputs )
+ self.wait_for_invocation_and_jobs( history_id, workflow_id, invocation_id )
+ details = self.dataset_populator.get_history_dataset_details( history_id, hid=0 )
+ last_item_hid = details["hid"]
+ assert last_item_hid == 7, "Expected 7 history items, got %s" % last_item_hid
+ content = self.dataset_populator.get_history_dataset_content( history_id, hid=0 )
+ self.assertEquals("10.0\n30.0\n20.0\n40.0\n", content )
def test_workflow_request( self ):
workflow = self.workflow_populator.load_workflow( name="test_for_queue" )
@@ -740,11 +742,14 @@
assert len( self._history_jobs( history_id ) ) == 2
self.__review_paused_steps( workflow_id, invocation_id, order_index=2, action=True )
+ self.wait_for_invocation_and_jobs( history_id, workflow_id, invocation_id )
+ assert len( self._history_jobs( history_id ) ) == 4
+
+ def wait_for_invocation_and_jobs( self, history_id, workflow_id, invocation_id, assert_ok=True ):
self.wait_for_invocation( workflow_id, invocation_id )
- time.sleep(1)
+ time.sleep(.5)
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
- time.sleep(1)
- assert len( self._history_jobs( history_id ) ) == 4
+ time.sleep(.5)
def test_cannot_run_inaccessible_workflow( self ):
workflow = self.workflow_populator.load_workflow( name="test_for_run_cannot_access" )
https://bitbucket.org/galaxy/galaxy-central/commits/0b16d383b7c3/
Changeset: 0b16d383b7c3
Branch: release_15.03
User: jmchilton
Date: 2015-03-03 14:37:30+00:00
Summary: Fix bug in workflows test for implicit connections between steps.
It would fail when being run with the rest of the suite and not on its own - because it was using the same id for the workflow id and invocation id - which is obviously wrong unless it is a completely fresh database :).
Affected #: 1 file
diff -r 814efb393019bec46ec9ac567d72d835210a982c -r 0b16d383b7c37e411bae2eed8a3c8681639e2dcd test/api/test_workflows.py
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -168,6 +168,7 @@
return RunJobsSummary(
history_id=history_id,
workflow_id=workflow_id,
+ invocation_id=invocation_id,
inputs=inputs,
jobs=jobs,
)
@@ -733,7 +734,7 @@
time.sleep( 2 )
history_id = run_summary.history_id
workflow_id = run_summary.workflow_id
- invocation_id = run_summary.workflow_id
+ invocation_id = run_summary.invocation_id
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
invocation = self._invocation_details( workflow_id, invocation_id )
assert invocation[ 'state' ] != 'scheduled'
@@ -1174,4 +1175,4 @@
'input_steps',
)
-RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'inputs', 'jobs'])
+RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'invocation_id', 'inputs', 'jobs'])
https://bitbucket.org/galaxy/galaxy-central/commits/6acef38c0c50/
Changeset: 6acef38c0c50
Branch: release_15.03
User: dan
Date: 2015-03-03 15:24:58+00:00
Summary: Add a 10 second timeout to loading data URLs for Tool Data Tables.
Affected #: 1 file
diff -r 0b16d383b7c37e411bae2eed8a3c8681639e2dcd -r 6acef38c0c504ee911f431325ae10df75c5862af lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -263,7 +263,7 @@
self.data = []
self.configure_and_load( config_element, tool_data_path, from_shed_config)
- def configure_and_load( self, config_element, tool_data_path, from_shed_config=False):
+ def configure_and_load( self, config_element, tool_data_path, from_shed_config=False, url_timeout=10 ):
"""
Configure and load table from an XML element.
"""
@@ -289,7 +289,7 @@
if filename:
tmp_file = NamedTemporaryFile( prefix='TTDT_URL_%s-' % self.name )
try:
- tmp_file.write( urlopen( filename ).read() )
+ tmp_file.write( urlopen( filename, timeout=url_timeout ).read() )
except Exception, e:
log.error( 'Error loading Data Table URL "%s": %s', filename, e )
continue
https://bitbucket.org/galaxy/galaxy-central/commits/f7babc8abdf0/
Changeset: f7babc8abdf0
Branch: release_15.03
User: dan
Date: 2015-03-03 15:49:12+00:00
Summary: When loading Dynamic Display application links, allow the application to load even if one set of links does not.
Affected #: 1 file
diff -r 6acef38c0c504ee911f431325ae10df75c5862af -r f7babc8abdf0801c5ea20dbd9753f26ce4481e07 lib/galaxy/datatypes/display_applications/application.py
--- a/lib/galaxy/datatypes/display_applications/application.py
+++ b/lib/galaxy/datatypes/display_applications/application.py
@@ -245,8 +245,11 @@
if link:
self.links[ link.id ] = link
for dynamic_links in elem.findall( 'dynamic_links' ):
- for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.app.datatypes_registry.build_sites ):
- self.links[ link.id ] = link
+ try:
+ for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.app.datatypes_registry.build_sites ):
+ self.links[ link.id ] = link
+ except Exception, e:
+ log.error( "Error loading a set of Dynamic Display Application links: %s", e )
def get_link( self, link_name, data, dataset_hash, user_hash, trans, app_kwds ):
#returns a link object with data knowledge to generate links
self._check_and_reload()
https://bitbucket.org/galaxy/galaxy-central/commits/5b5303124f42/
Changeset: 5b5303124f42
Branch: release_15.03
User: dan
Date: 2015-03-03 16:55:47+00:00
Summary: Fix for reports app not running mysql.
Affected #: 1 file
diff -r f7babc8abdf0801c5ea20dbd9753f26ce4481e07 -r 5b5303124f42eda46d90a736900042e5a27e2e80 lib/galaxy/webapps/reports/app.py
--- a/lib/galaxy/webapps/reports/app.py
+++ b/lib/galaxy/webapps/reports/app.py
@@ -25,7 +25,7 @@
db_url,
self.config.database_engine_options,
create_tables=True )
- self.targets_mysql = 'mysql' in self.config.database_connection
+ self.targets_mysql = self.config.database_connection and 'mysql' in self.config.database_connection
# Security helper
self.security = security.SecurityHelper( id_secret=self.config.id_secret )
# used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
https://bitbucket.org/galaxy/galaxy-central/commits/64266df71fa7/
Changeset: 64266df71fa7
Branch: release_15.03
User: carlfeberhard
Date: 2015-03-03 18:13:26+00:00
Summary: Fix to safari that still uses prefixed flexbox attributes
Affected #: 2 files
diff -r 5b5303124f42eda46d90a736900042e5a27e2e80 -r 64266df71fa71e8b3279be512f97798c96beead2 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -2119,7 +2119,7 @@
.annotated-history-panel table.list-items>tbody>tr>td>.list-item{border:0px}
.annotated-history-panel .empty-message{margin-top:8px}
.current-history-panel .list-item.history-content.current-content{border-left:5px solid #4E5777}
-.multi-panel-history{display:flex;flex-direction:column;}.multi-panel-history .flex-row-container,.multi-panel-history .flex-column-container{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;min-width:0px;min-height:0px;-webkit-align-items:stretch;-ms-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;-ms-align-content:stretch;align-content:stretch;-webkit-justify-content:flex-start;-ms-flex-pack:start;justify-content:flex-start}
+.multi-panel-history{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;-webkit-flex-direction:column;-ms-flex-direction:column;flex-direction:column;}.multi-panel-history .flex-row-container,.multi-panel-history .flex-column-container{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;min-width:0px;min-height:0px;-webkit-align-items:stretch;-ms-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;-ms-align-content:stretch;align-content:stretch;-webkit-justify-content:flex-start;-ms-flex-pack:start;justify-content:flex-start}
.multi-panel-history .flex-row-container{-webkit-flex-direction:column;-ms-flex-direction:column;flex-direction:column}
.multi-panel-history .flex-column-container{-webkit-flex-direction:row;-ms-flex-direction:row;flex-direction:row}
.multi-panel-history .flex-row,.multi-panel-history .flex-column{-webkit-flex:1 1 auto;-ms-flex:1 1 auto;flex:1 1 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}
@@ -2142,7 +2142,7 @@
.multi-panel-history .history-column:nth-child(2){margin-left:320px}
.multi-panel-history .history-column:last-child{margin-right:0px}
.multi-panel-history .history-column .dropdown-menu{z-index:inherit}
-.multi-panel-history .history-column .panel-controls{width:100%;height:24px;border-radius:3px;background-color:white;text-align:center;flex:0 0 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}.multi-panel-history .history-column .panel-controls .btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px}
+.multi-panel-history .history-column .panel-controls{width:100%;height:24px;border-radius:3px;background-color:white;text-align:center;-webkit-flex:0 0 auto;-ms-flex:0 0 auto;flex:0 0 auto;-webkit-align-self:auto;-ms-flex-item-align:auto;align-self:auto}.multi-panel-history .history-column .panel-controls .btn{height:20px;line-height:normal;font-size:90%;padding-top:0px;padding-bottom:0px}
.multi-panel-history .history-column .panel-controls .pull-left .btn{margin-right:4px}
.multi-panel-history .history-column .panel-controls .pull-right .btn{margin-left:4px}
.multi-panel-history .history-column .panel-controls .panel-menu{z-index:1}.multi-panel-history .history-column .panel-controls .panel-menu .dropdown-menu a{text-align:left}
diff -r 5b5303124f42eda46d90a736900042e5a27e2e80 -r 64266df71fa71e8b3279be512f97798c96beead2 static/style/src/less/history.less
--- a/static/style/src/less/history.less
+++ b/static/style/src/less/history.less
@@ -584,7 +584,13 @@
// for some reason, .flex-row-container below won't be applied to multi-panel-history since it's the enclosing node
// re-apply here
+ display: -webkit-box;
+ display: -webkit-flex;
+ display: -ms-flexbox;
display: flex;
+
+ -webkit-flex-direction: column;
+ -ms-flex-direction: column;
flex-direction: column;
.flex-row-container,
@@ -770,6 +776,8 @@
background-color: white;
text-align: center;
+ -webkit-flex: 0 0 auto;
+ -ms-flex: 0 0 auto;
flex: 0 0 auto;
-webkit-align-self: auto;
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
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1
0
[galaxyproject/usegalaxy-playbook] 84ee41: Update Main tool_data_table_conf.xml for igv_broad...
by GitHub 03 Mar '15
by GitHub 03 Mar '15
03 Mar '15
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 84ee415d5d0ba72081a9d9036970c4cd14b63232
https://github.com/galaxyproject/usegalaxy-playbook/commit/84ee415d5d0ba720…
Author: Daniel Blankenberg <blankenberg(a)users.noreply.github.com>
Date: 2015-03-03 (Tue, 03 Mar 2015)
Changed paths:
M files/galaxy/usegalaxy.org/config/tool_data_table_conf.xml
Log Message:
-----------
Update Main tool_data_table_conf.xml for igv_broad_genomes
1
0
[galaxyproject/usegalaxy-playbook] 017093: Update Test tool_data_table_conf.xml for igv_broad...
by GitHub 03 Mar '15
by GitHub 03 Mar '15
03 Mar '15
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 017093526f71e068110320c285ef64eb69780007
https://github.com/galaxyproject/usegalaxy-playbook/commit/017093526f71e068…
Author: Daniel Blankenberg <blankenberg(a)users.noreply.github.com>
Date: 2015-03-03 (Tue, 03 Mar 2015)
Changed paths:
M files/galaxy/test.galaxyproject.org/config/tool_data_table_conf.xml
Log Message:
-----------
Update Test tool_data_table_conf.xml for igv_broad_genomes
1
0
03 Mar '15
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 868e8d02cae300a263dcd49dadedeb23c6320ab2
https://github.com/galaxyproject/usegalaxy-playbook/commit/868e8d02cae300a2…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-03-03 (Tue, 03 Mar 2015)
Changed paths:
M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml
M stage/group_vars/all.yml
Log Message:
-----------
update test and mutable configs
1
0
45 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/02a1a5f1132f/
Changeset: 02a1a5f1132f
User: dan
Date: 2015-02-27 20:50:13+00:00
Summary: Allow External display applications to use Tool Data Tables.
Affected #: 7 files
diff -r 0468d285f89c799559926c94f300c42d05e8c47a -r 02a1a5f1132f722100097afef1be8d6b9725e783 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -88,7 +88,7 @@
# Load proprietary datatype converters and display applications.
self.installed_repository_manager.load_proprietary_converters_and_display_applications()
# Load datatype display applications defined in local datatypes_conf.xml
- self.datatypes_registry.load_display_applications()
+ self.datatypes_registry.load_display_applications( self )
# Load datatype converters defined in local datatypes_conf.xml
self.datatypes_registry.load_datatype_converters( self.toolbox )
# Load external metadata tool
diff -r 0468d285f89c799559926c94f300c42d05e8c47a -r 02a1a5f1132f722100097afef1be8d6b9725e783 lib/galaxy/datatypes/display_applications/application.py
--- a/lib/galaxy/datatypes/display_applications/application.py
+++ b/lib/galaxy/datatypes/display_applications/application.py
@@ -80,21 +80,57 @@
return True
class DynamicDisplayApplicationBuilder( object ):
- @classmethod
+
def __init__( self, elem, display_application, build_sites ):
- rval = []
filename = None
+ data_table = None
if elem.get( 'site_type', None ) is not None:
filename = build_sites.get( elem.get( 'site_type' ) )
else:
filename = elem.get( 'from_file', None )
- assert filename is not None, 'Filename and id attributes required for dynamic_links'
+ if filename is None:
+ data_table_name = elem.get( 'from_data_table', None )
+ if data_table_name:
+ data_table = display_application.app.tool_data_tables.get( data_table_name, None )
+ assert data_table is not None, 'Unable to find data table named "%s".' % data_table_name
+
+ assert filename is not None or data_table is not None,'Filename or data Table is required for dynamic_links.'
skip_startswith = elem.get( 'skip_startswith', None )
separator = elem.get( 'separator', '\t' )
- id_col = int( elem.get( 'id', None ) )
- name_col = int( elem.get( 'name', id_col ) )
+ id_col = elem.get( 'id', None )
+ try:
+ id_col = int( id_col )
+ except:
+ if data_table:
+ if id_col is None:
+ id_col = data_table.columns.get( 'id', None )
+ if id_col is None:
+ id_col = data_table.columns.get( 'value', None )
+ try:
+ id_col = int( id_col )
+ except:
+ # id is set to a string or None, use column by that name if available
+ id_col = data_table.columns.get( id_col, None )
+ id_col = int( id_col )
+ name_col = elem.get( 'name', None )
+ try:
+ name_col = int( name_col )
+ except:
+ if data_table:
+ if name_col is None:
+ name_col = data_table.columns.get( 'name', None )
+ else:
+ name_col = data_table.columns.get( name_col, None )
+ else:
+ name_col = None
+ if name_col is None:
+ name_col = id_col
+ max_col = max( id_col, name_col )
dynamic_params = {}
- max_col = max( id_col, name_col )
+ if data_table is not None:
+ max_col = max( [ max_col ] + data_table.columns.values() )
+ for key, value in data_table.columns.items():
+ dynamic_params[key] = { 'column': value, 'split': False, 'separator': ',' }
for dynamic_param in elem.findall( 'dynamic_param' ):
name = dynamic_param.get( 'name' )
value = int( dynamic_param.get( 'value' ) )
@@ -102,27 +138,38 @@
param_separator = dynamic_param.get( 'separator', ',' )
max_col = max( max_col, value )
dynamic_params[name] = { 'column': value, 'split': split, 'separator': param_separator }
- for line in open( filename ):
- if not skip_startswith or not line.startswith( skip_startswith ):
- line = line.rstrip( '\n\r' )
- if not line:
+ if filename:
+ data_iter = open( filename )
+ elif data_table:
+ version, data_iter = data_table.get_version_fields()
+ display_application.add_data_table_watch( data_table.name, version )
+ links = []
+ for line in data_iter:
+ if isinstance( line, basestring ):
+ if not skip_startswith or not line.startswith( skip_startswith ):
+ line = line.rstrip( '\n\r' )
+ if not line:
+ continue
+ fields = line.split( separator )
+ else:
continue
- fields = line.split( separator )
- if len( fields ) > max_col:
- new_elem = deepcopy( elem )
- new_elem.set( 'id', fields[id_col] )
- new_elem.set( 'name', fields[name_col] )
- dynamic_values = {}
- for key, attributes in dynamic_params.iteritems():
- value = fields[ attributes[ 'column' ] ]
- if attributes['split']:
- value = value.split( attributes['separator'] )
- dynamic_values[key] = value
- #now populate
- rval.append( DisplayApplicationLink.from_elem( new_elem, display_application, other_values = dynamic_values ) )
- else:
- log.warning( 'Invalid dynamic display application link specified in %s: "%s"' % ( filename, line ) )
- self.links = rval
+ else:
+ fields = line
+ if len( fields ) > max_col:
+ new_elem = deepcopy( elem )
+ new_elem.set( 'id', fields[id_col] )
+ new_elem.set( 'name', fields[name_col] )
+ dynamic_values = {}
+ for key, attributes in dynamic_params.iteritems():
+ value = fields[ attributes[ 'column' ] ]
+ if attributes['split']:
+ value = value.split( attributes['separator'] )
+ dynamic_values[key] = value
+ #now populate
+ links.append( DisplayApplicationLink.from_elem( new_elem, display_application, other_values = dynamic_values ) )
+ else:
+ log.warning( 'Invalid dynamic display application link specified in %s: "%s"' % ( filename, line ) )
+ self.links = links
def __iter__( self ):
return iter( self.links )
@@ -166,12 +213,12 @@
class DisplayApplication( object ):
@classmethod
- def from_file( cls, filename, datatypes_registry ):
- return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry, filename=filename )
+ def from_file( cls, filename, app ):
+ return cls.from_elem( parse_xml( filename ).getroot(), app, filename=filename )
@classmethod
- def from_elem( cls, elem, datatypes_registry, filename=None ):
+ def from_elem( cls, elem, app, filename=None ):
att_dict = cls._get_attributes_from_elem( elem )
- rval = DisplayApplication( att_dict['id'], att_dict['name'], datatypes_registry, att_dict['version'], filename=filename, elem=elem )
+ rval = DisplayApplication( att_dict['id'], att_dict['name'], app, att_dict['version'], filename=filename, elem=elem )
rval._load_links_from_elem( elem )
return rval
@classmethod
@@ -181,29 +228,32 @@
name = elem.get( 'name', display_id )
version = elem.get( 'version', None )
return dict( id=display_id, name=name, version=version )
- def __init__( self, display_id, name, datatypes_registry, version = None, filename=None, elem=None ):
+ def __init__( self, display_id, name, app, version = None, filename=None, elem=None ):
self.id = display_id
self.name = name
- self.datatypes_registry = datatypes_registry
+ self.app = app
if version is None:
version = "1.0.0"
self.version = version
self.links = odict()
self._filename = filename
self._elem = elem
+ self._data_table_versions = {}
def _load_links_from_elem( self, elem ):
for link_elem in elem.findall( 'link' ):
link = DisplayApplicationLink.from_elem( link_elem, self )
if link:
self.links[ link.id ] = link
for dynamic_links in elem.findall( 'dynamic_links' ):
- for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.datatypes_registry.build_sites ):
+ for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.app.datatypes_registry.build_sites ):
self.links[ link.id ] = link
def get_link( self, link_name, data, dataset_hash, user_hash, trans, app_kwds ):
#returns a link object with data knowledge to generate links
+ self._check_and_reload()
return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans, app_kwds )
def filter_by_dataset( self, data, trans ):
- filtered = DisplayApplication( self.id, self.name, self.datatypes_registry, version = self.version )
+ self._check_and_reload()
+ filtered = DisplayApplication( self.id, self.name, self.app, version = self.version )
for link_name, link_value in self.links.iteritems():
if link_value.filter_by_dataset( data, trans ):
filtered.links[link_name] = link_value
@@ -222,9 +272,24 @@
# clear old links
for key in self.links.keys():
del self.links[key]
+ #clear data table versions:
+ for key in self._data_table_versions.keys():
+ del self._data_table_versions[ key ]
# Set new attributes
for key, value in attr_dict.iteritems():
setattr( self, key, value )
# Load new links
self._load_links_from_elem( elem )
return self
+ def add_data_table_watch( self, table_name, version=None ):
+ self._data_table_versions[ table_name ] = version
+ def _requires_reload( self ):
+ for key, value in self._data_table_versions.iteritems():
+ table = self.app.tool_data_tables.get( key, None )
+ if table and not table.is_current_version( value ):
+ return True
+ return False
+ def _check_and_reload( self ):
+ if self._requires_reload():
+ self.reload()
+
diff -r 0468d285f89c799559926c94f300c42d05e8c47a -r 02a1a5f1132f722100097afef1be8d6b9725e783 lib/galaxy/datatypes/display_applications/parameters.py
--- a/lib/galaxy/datatypes/display_applications/parameters.py
+++ b/lib/galaxy/datatypes/display_applications/parameters.py
@@ -59,7 +59,7 @@
@property
def formats( self ):
if self.extensions:
- return tuple( map( type, map( self.link.display_application.datatypes_registry.get_datatype_by_extension, self.extensions ) ) )
+ return tuple( map( type, map( self.link.display_application.app.datatypes_registry.get_datatype_by_extension, self.extensions ) ) )
return None
def _get_dataset_like_object( self, other_values ):
#this returned object has file_name, state, and states attributes equivalent to a DatasetAssociation
diff -r 0468d285f89c799559926c94f300c42d05e8c47a -r 02a1a5f1132f722100097afef1be8d6b9725e783 lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -546,7 +546,7 @@
else:
self.log.exception( "Error loading converter (%s): %s" % ( converter_path, str( e ) ) )
- def load_display_applications( self, installed_repository_dict=None, deactivate=False ):
+ def load_display_applications( self, app, installed_repository_dict=None, deactivate=False ):
"""
If deactivate is False, add display applications from self.display_app_containers or
self.proprietary_display_app_containers to appropriate datatypes. If deactivate is
@@ -570,7 +570,7 @@
config_path = os.path.join( self.display_applications_path, display_file )
try:
inherit = galaxy.util.string_as_bool( display_app.get( 'inherit', 'False' ) )
- display_app = DisplayApplication.from_file( config_path, self )
+ display_app = DisplayApplication.from_file( config_path, app )
if display_app:
if display_app.id in self.display_applications:
if deactivate:
diff -r 0468d285f89c799559926c94f300c42d05e8c47a -r 02a1a5f1132f722100097afef1be8d6b9725e783 lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
--- a/lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
+++ b/lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
@@ -214,5 +214,5 @@
def load_installed_display_applications( self, installed_repository_dict, deactivate=False ):
"""Load or deactivate custom datatype display applications."""
- self.app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict,
+ self.app.datatypes_registry.load_display_applications( self.app, installed_repository_dict=installed_repository_dict,
deactivate=deactivate )
diff -r 0468d285f89c799559926c94f300c42d05e8c47a -r 02a1a5f1132f722100097afef1be8d6b9725e783 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -624,7 +624,7 @@
self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, installed_repository_dict=repository_dict )
if display_path:
# Load proprietary datatype display applications
- self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
+ self.app.datatypes_registry.load_display_applications( self.app, installed_repository_dict=repository_dict )
def handle_tool_shed_repositories( self, installation_dict ):
# The following installation_dict entries are all required.
diff -r 0468d285f89c799559926c94f300c42d05e8c47a -r 02a1a5f1132f722100097afef1be8d6b9725e783 lib/tool_shed/galaxy_install/tool_migration_manager.py
--- a/lib/tool_shed/galaxy_install/tool_migration_manager.py
+++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py
@@ -523,7 +523,7 @@
installed_repository_dict=repository_dict )
if display_path:
# Load proprietary datatype display applications
- self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
+ self.app.datatypes_registry.load_display_applications( self.app, installed_repository_dict=repository_dict )
basic_util.remove_dir( work_dir )
def install_repository( self, repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=False ):
https://bitbucket.org/galaxy/galaxy-central/commits/2158ee156a60/
Changeset: 2158ee156a60
User: dan
Date: 2015-02-27 20:50:28+00:00
Summary: Have IGV external display application load a set of links for available genomes via a tool data table that reads a URL (http://igv.broadinstitute.org/genomes/genomes.txt) The manually specified builds links should now be used to add additional builds, or for alias mapping (e.g. hg_g1k_v37-->b37).
Affected #: 4 files
diff -r 02a1a5f1132f722100097afef1be8d6b9725e783 -r 2158ee156a601bdc77e81d77363ebcd0f4b9f0f9 config/tool_data_table_conf.xml.sample
--- a/config/tool_data_table_conf.xml.sample
+++ b/config/tool_data_table_conf.xml.sample
@@ -65,4 +65,9 @@
<columns>value, path</columns><file path="tool-data/twobit.loc" /></table>
+ <!-- Available IGV builds, loaded from URL -->
+ <table name="igv_broad_genomes" comment_char="#">
+ <columns>name, url, value</columns>
+ <file url="http://igv.broadinstitute.org/genomes/genomes.txt" />
+ </table></tables>
diff -r 02a1a5f1132f722100097afef1be8d6b9725e783 -r 2158ee156a601bdc77e81d77363ebcd0f4b9f0f9 display_applications/igv/bam.xml
--- a/display_applications/igv/bam.xml
+++ b/display_applications/igv/bam.xml
@@ -93,7 +93,20 @@
#end if
</param></dynamic_links>
-
+
+
+ <dynamic_links from_data_table="igv_broad_genomes" skip_startswith="#" id="value" name="name">
+
+ <!-- Our input data table is one line per dbkey -->
+ <filter>${ $dataset.dbkey == $value }</filter>
+
+ <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+ <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bam… $bam_file.name )}</url>
+
+ <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
+ <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" />
+
+ </dynamic_links></display><!-- Dan Blankenberg -->
diff -r 02a1a5f1132f722100097afef1be8d6b9725e783 -r 2158ee156a601bdc77e81d77363ebcd0f4b9f0f9 display_applications/igv/vcf.xml
--- a/display_applications/igv/vcf.xml
+++ b/display_applications/igv/vcf.xml
@@ -93,7 +93,20 @@
#end if
</param></dynamic_links>
-
+
+
+ <dynamic_links from_data_table="igv_broad_genomes" skip_startswith="#" id="value" name="name">
+
+ <!-- Our input data table is one line per dbkey -->
+ <filter>${ $dataset.dbkey == $value }</filter>
+
+ <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+ <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bgz… $bgzip_file.name )}</url>
+
+ <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
+ <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
+
+ </dynamic_links></display><!-- Dan Blankenberg -->
diff -r 02a1a5f1132f722100097afef1be8d6b9725e783 -r 2158ee156a601bdc77e81d77363ebcd0f4b9f0f9 tool-data/shared/igv/igv_build_sites.txt.sample
--- a/tool-data/shared/igv/igv_build_sites.txt.sample
+++ b/tool-data/shared/igv/igv_build_sites.txt.sample
@@ -1,4 +1,4 @@
#site_id site_name site_url dbkey ivg_build_name
-web_link_main web current http://www.broadinstitute.org/igv/projects/current/igv.php hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
+web_link_main web current http://www.broadinstitute.org/igv/projects/current/igv.php hg_g1k_v37 b37
#web_jnlp_1.5 web 1.5 http://www.broadinstitute.org/igvdata/jws/prod hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
-#local_default local http://localhost:60151/load hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
\ No newline at end of file
+#local_default local http://localhost:60151/load hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
https://bitbucket.org/galaxy/galaxy-central/commits/9886c5e657d1/
Changeset: 9886c5e657d1
User: guerler
Date: 2015-02-28 06:33:15+00:00
Summary: ToolForm: Update biostar url for tool search
Affected #: 3 files
diff -r 2158ee156a601bdc77e81d77363ebcd0f4b9f0f9 -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 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
@@ -230,7 +230,7 @@
title : 'Search',
tooltip : 'Search help for this tool (Biostar)',
onclick : function() {
- window.open(options.biostar_url + '/t/' + options.id + '/');
+ window.open(options.biostar_url + '/local/search/page/?q=' + options.name);
}
});
};
diff -r 2158ee156a601bdc77e81d77363ebcd0f4b9f0f9 -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 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
@@ -230,7 +230,7 @@
title : 'Search',
tooltip : 'Search help for this tool (Biostar)',
onclick : function() {
- window.open(options.biostar_url + '/t/' + options.id + '/');
+ window.open(options.biostar_url + '/local/search/page/?q=' + options.name);
}
});
};
diff -r 2158ee156a601bdc77e81d77363ebcd0f4b9f0f9 -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 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(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.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})});
\ No newline at end of file
+define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(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.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/local/search/page/?q="+t.name)}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$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/071f254a1c43/
Changeset: 071f254a1c43
User: guerler
Date: 2015-02-28 08:01:14+00:00
Summary: ToolForm: Remove unnecessary helper class
Affected #: 9 files
diff -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 client/galaxy/scripts/mvc/tools/tools-content.js
--- a/client/galaxy/scripts/mvc/tools/tools-content.js
+++ /dev/null
@@ -1,55 +0,0 @@
-define(['utils/utils'], function(Utils){
- return Backbone.Model.extend({
- // initialize
- initialize: function(app) {
- this.summary = {};
- },
-
- /** Add new content elements
- */
- add: function(content_list) {
- // add/update content in summary list
- for (var i in content_list) {
- for (var j in content_list[i]) {
- var c = content_list[i][j];
- this.summary[c.id + '_' + c.src] = c;
- }
- }
- },
-
- /** Returns matched content from summary.
- */
- get: function(options) {
- return _.findWhere(this.summary, options) || {};
- },
-
- /** Get details of a content by id.
- */
- getDetails: function(options) {
- // check id
- if (!options.id || options.id === 'null') {
- options.success && options.success();
- return;
- }
-
- // create url
- var api_url = this.base_url + '/datasets/' + options.id;
- if (options.src == 'hdca') {
- api_url = this.base_url + '/dataset_collections/' + options.id;
- }
-
- // request details
- Utils.get({
- url : api_url,
- success : function(response) {
- options.success && options.success(response);
- },
- error : function(response) {
- options.success && options.success();
- console.debug('tools-content::getDetails() - Ajax request for content failed.');
- console.debug(response);
- }
- });
- }
- });
-});
\ No newline at end of file
diff -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 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
@@ -3,9 +3,9 @@
*/
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', 'mvc/tools/tools-template', 'mvc/tools/tools-section', 'mvc/tools/tools-tree'],
function(Utils, Deferred, Portlet, Ui, CitationModel, CitationView,
- Tools, ToolTemplate, ToolContent, ToolSection, ToolTree) {
+ Tools, ToolTemplate, ToolSection, ToolTree) {
// create form view
return Backbone.View.extend({
@@ -83,8 +83,8 @@
// creates a tree/json data structure from the input form
this.tree = new ToolTree(this);
- // request history content and build form
- this.content = new ToolContent(this);
+ // keeps track of history items
+ this.history = {};
// update model data
self.options.inputs = options && options.inputs;
diff -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 client/galaxy/scripts/mvc/tools/tools-select-content.js
--- a/client/galaxy/scripts/mvc/tools/tools-select-content.js
+++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js
@@ -179,6 +179,7 @@
/** Update content selector */
update: function(options) {
// update a particular select field
+ var self = this;
function _update(field, options) {
if (field) {
// identify available options
@@ -189,6 +190,8 @@
label: item.hid + ': ' + item.name,
value: item.id
});
+ // backup to local history
+ self.app.history[item.id + '_' + item.src] = item;
}
// update field
field.update(select_options);
@@ -199,9 +202,6 @@
_update(this.select_single, options.hda);
_update(this.select_multiple, options.hda);
_update(this.select_collection, options.hdca);
-
- // add to content list
- this.app.content.add(options);
},
/** Return the currently selected dataset values */
@@ -266,7 +266,7 @@
// append to dataset ids
for (var i in id_list) {
- var details = this.app.content.get({
+ var details = _.findWhere(this.app.history, {
id : id_list[i],
src : this.list[this.current].type
});
@@ -312,7 +312,7 @@
/** Assists in identifying the batch mode */
_batch: function() {
if (this.current == 'collection') {
- var hdca = this.app.content.get({
+ var hdca = _.findWhere(this.app.history, {
id : this._select().value(),
src : 'hdca'
});
diff -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 static/scripts/mvc/tools/tools-content.js
--- a/static/scripts/mvc/tools/tools-content.js
+++ /dev/null
@@ -1,55 +0,0 @@
-define(['utils/utils'], function(Utils){
- return Backbone.Model.extend({
- // initialize
- initialize: function(app) {
- this.summary = {};
- },
-
- /** Add new content elements
- */
- add: function(content_list) {
- // add/update content in summary list
- for (var i in content_list) {
- for (var j in content_list[i]) {
- var c = content_list[i][j];
- this.summary[c.id + '_' + c.src] = c;
- }
- }
- },
-
- /** Returns matched content from summary.
- */
- get: function(options) {
- return _.findWhere(this.summary, options) || {};
- },
-
- /** Get details of a content by id.
- */
- getDetails: function(options) {
- // check id
- if (!options.id || options.id === 'null') {
- options.success && options.success();
- return;
- }
-
- // create url
- var api_url = this.base_url + '/datasets/' + options.id;
- if (options.src == 'hdca') {
- api_url = this.base_url + '/dataset_collections/' + options.id;
- }
-
- // request details
- Utils.get({
- url : api_url,
- success : function(response) {
- options.success && options.success(response);
- },
- error : function(response) {
- options.success && options.success();
- console.debug('tools-content::getDetails() - Ajax request for content failed.');
- console.debug(response);
- }
- });
- }
- });
-});
\ No newline at end of file
diff -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 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
@@ -3,9 +3,9 @@
*/
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', 'mvc/tools/tools-template', 'mvc/tools/tools-section', 'mvc/tools/tools-tree'],
function(Utils, Deferred, Portlet, Ui, CitationModel, CitationView,
- Tools, ToolTemplate, ToolContent, ToolSection, ToolTree) {
+ Tools, ToolTemplate, ToolSection, ToolTree) {
// create form view
return Backbone.View.extend({
@@ -83,8 +83,8 @@
// creates a tree/json data structure from the input form
this.tree = new ToolTree(this);
- // request history content and build form
- this.content = new ToolContent(this);
+ // keeps track of history items
+ this.history = {};
// update model data
self.options.inputs = options && options.inputs;
diff -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 static/scripts/mvc/tools/tools-select-content.js
--- a/static/scripts/mvc/tools/tools-select-content.js
+++ b/static/scripts/mvc/tools/tools-select-content.js
@@ -179,6 +179,7 @@
/** Update content selector */
update: function(options) {
// update a particular select field
+ var self = this;
function _update(field, options) {
if (field) {
// identify available options
@@ -189,6 +190,8 @@
label: item.hid + ': ' + item.name,
value: item.id
});
+ // backup to local history
+ self.app.history[item.id + '_' + item.src] = item;
}
// update field
field.update(select_options);
@@ -199,9 +202,6 @@
_update(this.select_single, options.hda);
_update(this.select_multiple, options.hda);
_update(this.select_collection, options.hdca);
-
- // add to content list
- this.app.content.add(options);
},
/** Return the currently selected dataset values */
@@ -266,7 +266,7 @@
// append to dataset ids
for (var i in id_list) {
- var details = this.app.content.get({
+ var details = _.findWhere(this.app.history, {
id : id_list[i],
src : this.list[this.current].type
});
@@ -312,7 +312,7 @@
/** Assists in identifying the batch mode */
_batch: function() {
if (this.current == 'collection') {
- var hdca = this.app.content.get({
+ var hdca = _.findWhere(this.app.history, {
id : this._select().value(),
src : 'hdca'
});
diff -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 static/scripts/packed/mvc/tools/tools-content.js
--- a/static/scripts/packed/mvc/tools/tools-content.js
+++ /dev/null
@@ -1,1 +0,0 @@
-define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.summary={}},add:function(e){for(var d in e){for(var b in e[d]){var f=e[d][b];this.summary[f.id+"_"+f.src]=f}}},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})}})});
\ No newline at end of file
diff -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 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(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.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/local/search/page/?q="+t.name)}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$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.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})});
\ No newline at end of file
+define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-section","mvc/tools/tools-tree"],function(f,g,e,j,h,a,d,c,i,b){return Backbone.View.extend({initialize:function(k){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=f.merge(k,this.optionsDefault);console.debug(this.options);var l=parent.Galaxy;if(l&&l.modal){this.modal=l.modal}else{this.modal=new j.Modal.View()}if(l&&l.currUser){this.is_admin=l.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new g();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(m){var k=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.history={};k.options.inputs=m&&m.inputs;this._renderForm(m);var l=this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){k.deferred.reset();k.deferred.execute(function(){var n=k.tree.finalize();if(!_.isEqual(n,l)){l=n;k._updateModel($.extend({},l))}})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}})},reciept:function(k){$(this.container).empty();$(this.container).append(k)},highlight:function(l,m,k){var n=this.element_list[l];if(n){n.error(m||"Please verify this parameter.");if(!k){$("html, body").animate({scrollTop:n.$el.offset().top-20},500)}}},_errors:function(m){this.trigger("reset");if(m&&m.errors){var n=this.tree.matchResponse(m.errors);for(var l in this.element_list){var k=this.element_list[l];if(n[l]){this.highlight(l,n[l],true)}}}},_renderForm:function(s){var r=this;this.message=new j.Message();var l=new j.ButtonMenu({icon:"fa-cubes",title:(!s.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(s.versions&&s.versions.length>1){for(var n in s.versions){var p=s.versions[n];if(p!=s.version){l.addMenu({title:"Switch to "+p,version:p,icon:"fa-cube",onclick:function(){r.options.id=r.options.id.replace(r.options.version,this.version);r.options.version=this.version;r.deferred.reset();r.deferred.execute(function(){r._buildModel()})}})}}}else{l.$el.hide()}var o=new j.ButtonMenu({icon:"fa-caret-down",title:(!s.narrow&&"Options")||null,tooltip:"View available options"});if(s.biostar_url){o.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(s.biostar_url+"/p/new/post/")}});o.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(s.biostar_url+"/t/"+s.id+"/")}})}o.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+s.id)}});if(this.is_admin){o.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+s.id+"/download"}})}if(s.requirements&&s.requirements.length>0){o.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;r.message.update({persistent:true,message:c.requirements(s),status:"info"})}else{this.visible=false;r.message.update({message:""})}}})}if(this.options.sharable_url){o.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(r.options.sharable_url)}})}this.section=new i.View(r,{inputs:s.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new e.View({icon:"fa-wrench",title:"<b>"+s.name+"</b> "+s.description+" (Galaxy Tool Version "+s.version+")",cls:this.options.cls_portlet,operations:{menu:o,versions:l},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(s.help!=""){this.$el.append(c.help(s.help))}if(s.citations){var q=$("<div/>");var k=new h.ToolCitationCollection();k.tool_id=s.id;var m=new a.CitationListView({el:q,collection:k});m.render();k.fetch();this.$el.append(q)}if(s.message){this.message.update({persistent:true,status:"warning",message:s.message})}console.debug("tools-form-base::initialize() - Completed.")}})});
diff -r 9886c5e657d1f004c8c0f362cb4f62f1326d0c74 -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 static/scripts/packed/mvc/tools/tools-select-content.js
--- a/static/scripts/packed/mvc/tools/tools-select-content.js
+++ b/static/scripts/packed/mvc/tools/tools-select-content.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(h){var f=this;function g(m,j){if(m){var n=[];for(var k in j){var l=j[k];n.push({label:l.hid+": "+l.name,value:l.id});f.app.history[l.id+"_"+l.src]=l}m.update(n)}}g(this.select_single,h.hda);g(this.select_multiple,h.hda);g(this.select_collection,h.hdca)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=_.findWhere(this.app.history,{id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=_.findWhere(this.app.history,{id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/d0bfc1c72bab/
Changeset: d0bfc1c72bab
User: guerler
Date: 2015-02-28 09:30:14+00:00
Summary: ToolForm: Do not show submission error if user closes progress modal
Affected #: 3 files
diff -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 -r d0bfc1c72bab6a8f390ee44f4d052810c2b94900 client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -34,7 +34,13 @@
console.debug(job_def);
// show progress modal
- this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: { 'Close' : function () {self.app.modal.hide();} }});
+ var user_is_waiting = true;
+ this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
+ 'Close' : function () {
+ self.app.modal.hide();
+ user_is_waiting = false;
+ }
+ }});
// post job
Utils.request({
@@ -57,7 +63,7 @@
} else {
// show error message with details
console.debug(response);
- self.app.modal.show({
+ user_is_waiting && self.app.modal.show({
title : 'Job submission failed',
body : ToolTemplate.error(job_def),
buttons : {
diff -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 -r d0bfc1c72bab6a8f390ee44f4d052810c2b94900 static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -34,7 +34,13 @@
console.debug(job_def);
// show progress modal
- this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: { 'Close' : function () {self.app.modal.hide();} }});
+ var user_is_waiting = true;
+ this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
+ 'Close' : function () {
+ self.app.modal.hide();
+ user_is_waiting = false;
+ }
+ }});
// post job
Utils.request({
@@ -57,7 +63,7 @@
} else {
// show error message with details
console.debug(response);
- self.app.modal.show({
+ user_is_waiting && self.app.modal.show({
title : 'Job submission failed',
body : ToolTemplate.error(job_def),
buttons : {
diff -r 071f254a1c43fbde264dc196c9941d5ce5afcf68 -r d0bfc1c72bab6a8f390ee44f4d052810c2b94900 static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var d={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.reciept(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c.app.highlight(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var e={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(e)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(e);var d=true;this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide();d=false}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:e,success:function(f){c.app.modal.hide();c.app.reciept(a.success(f));c._refreshHdas()},error:function(f,h){c.app.modal.hide();if(f&&f.message&&f.message.data){var i=c.app.tree.matchResponse(f.message.data);for(var g in i){c.app.highlight(g,i[g]);break}}else{console.debug(f);d&&c.app.modal.show({title:"Job submission failed",body:a.error(e),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/a4bb127f32c3/
Changeset: a4bb127f32c3
User: guerler
Date: 2015-02-28 09:37:37+00:00
Summary: ToolForm: Use default closing behaviour for progress modal
Affected #: 3 files
diff -r d0bfc1c72bab6a8f390ee44f4d052810c2b94900 -r a4bb127f32c3c2b85f02e138f4ac13475cd15704 client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -35,7 +35,7 @@
// show progress modal
var user_is_waiting = true;
- this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
+ this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: {
'Close' : function () {
self.app.modal.hide();
user_is_waiting = false;
diff -r d0bfc1c72bab6a8f390ee44f4d052810c2b94900 -r a4bb127f32c3c2b85f02e138f4ac13475cd15704 static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -35,7 +35,7 @@
// show progress modal
var user_is_waiting = true;
- this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
+ this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: {
'Close' : function () {
self.app.modal.hide();
user_is_waiting = false;
diff -r d0bfc1c72bab6a8f390ee44f4d052810c2b94900 -r a4bb127f32c3c2b85f02e138f4ac13475cd15704 static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var e={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(e)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(e);var d=true;this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide();d=false}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:e,success:function(f){c.app.modal.hide();c.app.reciept(a.success(f));c._refreshHdas()},error:function(f,h){c.app.modal.hide();if(f&&f.message&&f.message.data){var i=c.app.tree.matchResponse(f.message.data);for(var g in i){c.app.highlight(g,i[g]);break}}else{console.debug(f);d&&c.app.modal.show({title:"Job submission failed",body:a.error(e),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var e={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(e)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(e);var d=true;this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide();d=false}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:e,success:function(f){c.app.modal.hide();c.app.reciept(a.success(f));c._refreshHdas()},error:function(f,h){c.app.modal.hide();if(f&&f.message&&f.message.data){var i=c.app.tree.matchResponse(f.message.data);for(var g in i){c.app.highlight(g,i[g]);break}}else{console.debug(f);d&&c.app.modal.show({title:"Job submission failed",body:a.error(e),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/24ff3e302d60/
Changeset: 24ff3e302d60
User: guerler
Date: 2015-02-28 09:30:14+00:00
Summary: ToolForm: Do not show submission error if user closes progress modal
Affected #: 3 files
diff -r a4bb127f32c3c2b85f02e138f4ac13475cd15704 -r 24ff3e302d60f610db061461417d2f0ba31fda30 client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -35,7 +35,7 @@
// show progress modal
var user_is_waiting = true;
- this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: {
+ this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
'Close' : function () {
self.app.modal.hide();
user_is_waiting = false;
@@ -157,4 +157,4 @@
}
});
-});
\ No newline at end of file
+});
diff -r a4bb127f32c3c2b85f02e138f4ac13475cd15704 -r 24ff3e302d60f610db061461417d2f0ba31fda30 static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -35,7 +35,7 @@
// show progress modal
var user_is_waiting = true;
- this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: {
+ this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
'Close' : function () {
self.app.modal.hide();
user_is_waiting = false;
@@ -157,4 +157,4 @@
}
});
-});
\ No newline at end of file
+});
diff -r a4bb127f32c3c2b85f02e138f4ac13475cd15704 -r 24ff3e302d60f610db061461417d2f0ba31fda30 static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var e={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(e)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(e);var d=true;this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide();d=false}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:e,success:function(f){c.app.modal.hide();c.app.reciept(a.success(f));c._refreshHdas()},error:function(f,h){c.app.modal.hide();if(f&&f.message&&f.message.data){var i=c.app.tree.matchResponse(f.message.data);for(var g in i){c.app.highlight(g,i[g]);break}}else{console.debug(f);d&&c.app.modal.show({title:"Job submission failed",body:a.error(e),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var e={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(e)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(e);var d=true;this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide();d=false}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:e,success:function(f){c.app.modal.hide();c.app.reciept(a.success(f));c._refreshHdas()},error:function(f,h){c.app.modal.hide();if(f&&f.message&&f.message.data){var i=c.app.tree.matchResponse(f.message.data);for(var g in i){c.app.highlight(g,i[g]);break}}else{console.debug(f);d&&c.app.modal.show({title:"Job submission failed",body:a.error(e),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
https://bitbucket.org/galaxy/galaxy-central/commits/3570617751c5/
Changeset: 3570617751c5
User: guerler
Date: 2015-02-28 09:37:37+00:00
Summary: ToolForm: Use default closing behaviour for progress modal
Affected #: 3 files
diff -r 24ff3e302d60f610db061461417d2f0ba31fda30 -r 3570617751c579e323725444a432415d7af3607e client/galaxy/scripts/mvc/tools/tools-jobs.js
--- a/client/galaxy/scripts/mvc/tools/tools-jobs.js
+++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js
@@ -35,7 +35,7 @@
// show progress modal
var user_is_waiting = true;
- this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
+ this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: {
'Close' : function () {
self.app.modal.hide();
user_is_waiting = false;
diff -r 24ff3e302d60f610db061461417d2f0ba31fda30 -r 3570617751c579e323725444a432415d7af3607e static/scripts/mvc/tools/tools-jobs.js
--- a/static/scripts/mvc/tools/tools-jobs.js
+++ b/static/scripts/mvc/tools/tools-jobs.js
@@ -35,7 +35,7 @@
// show progress modal
var user_is_waiting = true;
- this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: {
+ this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: {
'Close' : function () {
self.app.modal.hide();
user_is_waiting = false;
diff -r 24ff3e302d60f610db061461417d2f0ba31fda30 -r 3570617751c579e323725444a432415d7af3607e static/scripts/packed/mvc/tools/tools-jobs.js
--- a/static/scripts/packed/mvc/tools/tools-jobs.js
+++ b/static/scripts/packed/mvc/tools/tools-jobs.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var e={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(e)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(e);var d=true;this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide();d=false}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:e,success:function(f){c.app.modal.hide();c.app.reciept(a.success(f));c._refreshHdas()},error:function(f,h){c.app.modal.hide();if(f&&f.message&&f.message.data){var i=c.app.tree.matchResponse(f.message.data);for(var g in i){c.app.highlight(g,i[g]);break}}else{console.debug(f);d&&c.app.modal.show({title:"Job submission failed",body:a.error(e),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
+define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(c){this.app=c},submit:function(){var c=this;var e={tool_id:this.app.options.id,tool_version:this.app.options.version,inputs:this.app.tree.finalize()};this.app.trigger("reset");if(!this._validation(e)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(e);var d=true;this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide();d=false}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:e,success:function(f){c.app.modal.hide();c.app.reciept(a.success(f));c._refreshHdas()},error:function(f,h){c.app.modal.hide();if(f&&f.message&&f.message.data){var i=c.app.tree.matchResponse(f.message.data);for(var g in i){c.app.highlight(g,i[g]);break}}else{console.debug(f);d&&c.app.modal.show({title:"Job submission failed",body:a.error(e),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&f==null){this.app.highlight(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this.app.highlight(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this.app.highlight(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})});
https://bitbucket.org/galaxy/galaxy-central/commits/11d5bb0dd643/
Changeset: 11d5bb0dd643
User: guerler
Date: 2015-02-28 10:01:55+00:00
Summary: Parameters: Remove unused uncoded id from data parameter dictionaries
Affected #: 1 file
diff -r 3570617751c579e323725444a432415d7af3607e -r 11d5bb0dd643c90472bebd5cc2b2d000c9ace85c lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2172,7 +2172,6 @@
m = match.hda
d['options']['hda'].append({
'id' : trans.security.encode_id( m.id ),
- 'id_uncoded' : m.id,
'hid' : m.hid,
'name' : m.name,
'src' : 'hda'
@@ -2184,7 +2183,6 @@
if dataset_collection_matcher.hdca_match( hdca, reduction=multiple ):
d['options']['hdca'].append({
'id' : trans.security.encode_id( hdca.id ),
- 'id_uncoded' : hdca.id,
'hid' : hdca.hid,
'name' : hdca.name,
'src' : 'hdca'
@@ -2391,7 +2389,6 @@
for hdca in self.match_collections( trans, history, dataset_matcher ):
d['options']['hdca'].append({
'id' : trans.security.encode_id( hdca.id ),
- 'id_uncoded' : hdca.id,
'hid' : hdca.hid,
'name' : hdca.name,
'src' : 'hdca'
@@ -2402,7 +2399,6 @@
subcollection_type = self._history_query( trans ).collection_type_description.collection_type
d['options']['hdca'].append({
'id' : trans.security.encode_id( hdca.id ),
- 'id_uncoded' : hdca.id,
'hid' : hdca.hid,
'name' : hdca.name,
'src' : 'hdca',
https://bitbucket.org/galaxy/galaxy-central/commits/56e108003f4e/
Changeset: 56e108003f4e
User: guerler
Date: 2015-02-28 17:12:10+00:00
Summary: Charts: Add data point labels to all nvd3 charts (without this gene expression analysis using scatter plots is not very useful)
Affected #: 6 files
diff -r 11d5bb0dd643c90472bebd5cc2b2d000c9ace85c -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors
// Underscore may be freely distributed under the MIT license.
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t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var 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class="ui-options-list drilldown-container" id="'+e.id+'"/>'}});return{View:n}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1),value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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n=this.$("#button-"+e),r=this.$("#subgroup-"+e);n.data("is_expanded",t),t?(r.fadeIn("fast"),n.removeClass("toggle-expand"),n.addClass("toggle")):(r.hide(),n.removeClass("toggle"),n.addClass("toggle-expand"))},_templateOptions:function(t){function r(e,t){var r=e.find("#button-"+t);r.on("click",function(){n._setState(t,!r.data("is_expanded"))})}function s(t,o,u){u=u||[];for(i in o){var a=o[i],f=a.options.length>0,l=u.slice(0);n.header_index[a.value]=l.slice(0);var c=$("<div/>");if(f){var h=e.uuid(),p=$('<span id="button-'+h+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'),d=$('<div id="subgroup-'+h+'" style="display: none; margin-left: 25px;"/>');l.push(h);var v=$("<div/>");v.append(p),v.append(n._templateOption({label:a.name,value:a.value})),c.append(v),s(d,a.options,l),c.append(d),r(c,h)}else c.append(n._templateOption({label:a.name,value:a.value}));t.append(c)}}var n=this;this.header_index={};var o=$("<div/>");return s(o,t),o},_template:function(e){return'<div 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r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,t,n,r,i,s,o,u){var a=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),l=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},setIcon:function(e){this.$("i").removeClass(this.options.icon).addClass(e),this.options.icon=e},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),d=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>"),this.options.message&&this.update(this.options)},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn(),this.timeout&&window.clearTimeout(this.timeout);if(!t.persistent){var n=this;this.timeout=window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),v=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),g=Backbone.View.extend({initialize:function(e){this.options=e,this.setElement(this._template(this.options)),this.options.value!==undefined&&this.value(this.options.value)},value:function(e){return e!==undefined&&this.$("hidden").val(e),this.$("hidden").val()},_template:function(e){var t='<div id="'+e.id+'" >';return e.info&&(t+="<div>"+e.info+"</div>"),t+='<hidden value="'+e.value+'"/>'+"</div>",t}});return{Anchor:p,Button:c,ButtonIcon:h,ButtonCheck:o,ButtonMenu:s,Icon:l,Image:a,Input:m,Label:f,Message:d,Modal:u,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:v,Select:t,Hidden:g,Slider:n,Drilldown:i}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&!o.is_text&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,50);var r=$("body").css("overflow");this.$el.on("mouseover",function(){$("body").css("overflow","hidden")}).on("mouseout",function(){$("body").css("overflow",r)}),this._createContainer("div");var i=this;this.chart.on("redraw",function(){i._draw(i.chart)}),this.chart.on("set:state",function(){var e=i.$el.find("#info"),t=i.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(i.chart.get("state_info"));var r=i.chart.get("state");switch(r){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(n,r){this.app=n;var i=this;this.chart=this.app.chart,this.group=r.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){i.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var s=$("<div/>");s.append((new t.Label({title:"Provide a label:"})).$el),s.append(this.group_key.$el.addClass("ui-margin-bottom")),s.append((new t.Label({title:"Select columns:"})).$el.addClass("ui-margin-top")),s.append(this.table.$el.addClass("ui-margin-bottom")),this.setElement(s);var i=this;this.chart.on("change:dataset_id",function(){i._refreshTable()}),this.chart.on("change:type",function(){i._refreshTable()}),this.group.on("change:key",function(){i._refreshGroupKey()}),this.group.on("change",function(){i._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=r.is_text,c=[],h=n[e];o&&c.push({label:"Column: Row Number",value:"auto"}),f&&c.push({label:"Column: None",value:"zero"});var p=t.metadata_column_types;for(var d in p){var v=!1;p[d]=="int"||p[d]=="float"?v=u:v=l||s,v&&c.push({label:"Column: "+(parseInt(d)+1),value:d})}h.update(c),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!h.exists(this.group.get(e))){var m=h.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+m+'".'),this.group.set(e,m)}h.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){h.value(i.group.get(e))}),h.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),h.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),e!=this.group_key.value()&&this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(this.table_title.$el),s.append(this.table.$el),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var 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t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return arguments.length?(n=e,g):n},g.height=function(e){return arguments.length?(r=e,g):r},g.clipEdge=function(e){return arguments.length?(h=e,g):h},g.color=function(t){return arguments.length?(i=e.utils.getColor(t),g):i},g.offset=function(e){return arguments.length?(f=e,g):f},g.order=function(e){return arguments.length?(l=e,g):l},g.style=function(e){if(!arguments.length)return a;a=e;switch(a){case"stack":g.offset("zero"),g.order("default");break;case"stream":g.offset("wiggle"),g.order("inside-out");break;case"stream-center":g.offset("silhouette"),g.order("inside-out");break;case"expand":g.offset("expand"),g.order("default");break;case"stack_percent":g.offset(g.d3_stackedOffset_stackPercent),g.order("default")}return g},g.interpolate=function(e){return arguments.length?(c=e,g):c},g},e.models.stackedAreaChart=function(){function M(y){return y.each(function(y){var 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k.indexOf(e.metaKey)!==-1}),s.width(C).color(["#444","#444","#444"]),I.select(".nv-controlsWrap").datum(R).call(s),u.top!=Math.max(s.height(),i.height())&&(u.top=Math.max(s.height(),i.height()),P=(f||parseInt(A.style("height"))||400)-u.top-u.bottom),I.select(".nv-controlsWrap").attr("transform","translate(0,"+ -u.top+")")}j.attr("transform","translate("+u.left+","+u.top+")"),v&&I.select(".nv-y.nv-axis").attr("transform","translate("+D+",0)"),m&&(o.width(D).height(P).margin({left:u.left,top:u.top}).svgContainer(A).xScale(b),j.select(".nv-interactive").call(o)),t.width(D).height(P);var U=I.select(".nv-stackedWrap").datum(y);U.call(t),p&&(n.scale(b).ticks(D/100).tickSize(-P,0),I.select(".nv-x.nv-axis").attr("transform","translate(0,"+P+")"),I.select(".nv-x.nv-axis").call(n)),d&&(r.scale(w).ticks(t.offset()=="wiggle"?0:P/36).tickSize(-D,0).setTickFormat(t.style()=="expand"||t.style()=="stack_percent"?d3.format("%"):E),I.select(".nv-y.nv-axis").call(r)),t.dispatch.on("areaClick.toggle",function(e){y.filter(function(e){return!e.disabled}).length===1?y.forEach(function(e){e.disabled=!1}):y.forEach(function(t,n){t.disabled=n!=e.seriesIndex}),S.disabled=y.map(function(e){return!!e.disabled}),N.stateChange(S),M.update()}),i.dispatch.on("stateChange",function(e){S.disabled=e.disabled,N.stateChange(S),M.update()}),s.dispatch.on("legendClick",function(e,n){if(!e.disabled)return;R=R.map(function(e){return e.disabled=!0,e}),e.disabled=!1,t.style(e.style),S.style=t.style(),N.stateChange(S),M.update()}),o.dispatch.on("elementMousemove",function(i){t.clearHighlights();var s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return r.tickFormat()(e)};o.tooltip.position({left:f+u.left,top:i.mouseY+u.top}).chartContainer(_.parentNode).enabled(g).valueFormatter(m).data({value:v,series:c})(),o.renderGuideLine(f)}),o.dispatch.on("elementMouseout",function(e){N.tooltipHide(),t.clearHighlights()}),N.on("tooltipShow",function(e){g&&O(e,_.parentNode)}),N.on("changeState",function(e){typeof e.disabled!="undefined"&&y.length===e.disabled.length&&(y.forEach(function(t,n){t.disabled=e.disabled[n]}),S.disabled=e.disabled),typeof e.style!="undefined"&&t.style(e.style),M.update()})}),M}var t=e.models.stackedArea(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.interactiveGuideline(),u={top:30,right:25,bottom:50,left:60},a=null,f=null,l=e.utils.defaultColor(),c=!0,h=!0,p=!0,d=!0,v=!1,m=!1,g=!0,y=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" on "+t+"</p>"},b,w,E=d3.format(",.2f"),S={style:t.style()},x=null,T="No Data Available.",N=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),C=250,k=["Stacked","Stream","Expanded"],L={},A=0;n.orient("bottom").tickPadding(7),r.orient(v?"right":"left"),s.updateState(!1);var O=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),a=n.tickFormat()(t.x()(i.point,i.pointIndex)),f=r.tickFormat()(t.y()(i.point,i.pointIndex)),l=y(i.series.key,a,f,i,M);e.tooltip.show([o,u],l,i.value<0?"n":"s",null,s)};return t.dispatch.on("tooltipShow",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],N.tooltipShow(e)}),t.dispatch.on("tooltipHide",function(e){N.tooltipHide(e)}),N.on("tooltipHide",function(){g&&e.tooltip.cleanup()}),M.dispatch=N,M.stacked=t,M.legend=i,M.controls=s,M.xAxis=n,M.yAxis=r,M.interactiveLayer=o,d3.rebind(M,t,"x","y","size","xScale","yScale","xDomain","yDomain","xRange","yRange","sizeDomain","interactive","useVoronoi","offset","order","style","clipEdge","forceX","forceY","forceSize","interpolate"),M.options=e.utils.optionsFunc.bind(M),M.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,M):u},M.width=function(e){return arguments.length?(a=e,M):a},M.height=function(e){return arguments.length?(f=e,M):f},M.color=function(n){return arguments.length?(l=e.utils.getColor(n),i.color(l),t.color(l),M):l},M.showControls=function(e){return arguments.length?(c=e,M):c},M.showLegend=function(e){return arguments.length?(h=e,M):h},M.showXAxis=function(e){return arguments.length?(p=e,M):p},M.showYAxis=function(e){return arguments.length?(d=e,M):d},M.rightAlignYAxis=function(e){return arguments.length?(v=e,r.orient(e?"right":"left"),M):v},M.useInteractiveGuideline=function(e){return arguments.length?(m=e,e===!0&&(M.interactive(!1),M.useVoronoi(!1)),M):m},M.tooltip=function(e){return arguments.length?(y=e,M):y},M.tooltips=function(e){return arguments.length?(g=e,M):g},M.tooltipContent=function(e){return arguments.length?(y=e,M):y},M.state=function(e){return arguments.length?(S=e,M):S},M.defaultState=function(e){return arguments.length?(x=e,M):x},M.noData=function(e){return arguments.length?(T=e,M):T},M.transitionDuration=function(e){return arguments.length?(A=e,M):A},M.controlsData=function(e){return arguments.length?(k=e,M):k},M.controlLabels=function(e){return arguments.length?typeof e!="object"?L:(L=e,M):L},r.setTickFormat=r.tickFormat,r.tickFormat=function(e){return arguments.length?(E=e,r):E},M}}(),define("plugin/plugins/nvd3/nv.d3",function(){}),define("plugin/charts/nvd3/common/config",["plugin/charts/forms/default","plugin/plugins/nvd3/nv.d3"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"NVD3",tag:"svg",keywords:"small",columns:{tooltip:{title:"Data point labels",is_text:!0,is_numeric:!0,is_auto:!0}}})}),define("plugin/charts/nvd3/bar/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/bar_stacked/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Stacked",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/bar_horizontal/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}},columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/bar_horizontal_stacked/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Stacked horizontal",category:"Bar diagrams",settings:{x_axis_type:{init:"hide"}},columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/line_focus/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus",category:"Others",zoomable:"native",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/pie/config",["plugin/plugins/nvd3/nv.d3"],function(){return $.extend(!0,{},{title:"Pie chart",category:"Area charts",library:"NVD3",tag:"svg",keywords:"small",columns:{label:{title:"Labels",is_label:!0,is_auto:!0},y:{title:"Values",is_numeric:!0}},settings:{main_separator:{type:"separator",title:"Pie chart settings"},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing --",value:"hide",hide:"label_outside"},{label:"Label column",value:"key",show:"label_outside"},{label:"Value column",value:"value",show:"label_outside"},{label:"Percentage",value:"percent",show:"label_outside"}]},label_outside:{title:"Show outside",info:"Would you like to show labels outside the donut?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{init:"true",hide:!0}}})}),define("plugin/charts/nvd3/stackedarea_full/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Expanded",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea_stream/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Stream",category:"Area charts",zoomable:!0,keywords:"default small",showmaxmin:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/histogram/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{x_axis_label:{init:"Values"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_precision:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/scatter/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","utils/deferred","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})});
\ No newline at end of file
diff -r 11d5bb0dd643c90472bebd5cc2b2d000c9ace85c -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
@@ -4,7 +4,15 @@
category : '',
library : 'NVD3',
tag : 'svg',
- keywords : 'small'
+ keywords : 'small',
+ columns : {
+ tooltip : {
+ title : 'Data point labels',
+ is_text : true,
+ is_numeric : true,
+ is_auto : true
+ }
+ }
});
});
\ No newline at end of file
diff -r 11d5bb0dd643c90472bebd5cc2b2d000c9ace85c -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
@@ -15,71 +15,76 @@
options.render = function(canvas_id, groups) {
return self.render(canvas_id, groups)
};
-
+
// call panel helper
Tools.panelHelper(app, options);
},
-
+
// render
render : function(canvas_id, groups) {
var chart = this.options.chart;
var type = this.options.type;
var makeConfig = this.options.makeConfig;
-
+
// create nvd3 model
var d3chart = nv.models[type]()
-
+
// request data
var self = this;
nv.addGraph(function() {
try {
// x axis label
d3chart.xAxis.axisLabel(chart.settings.get('x_axis_label'));
-
+
// y axis label
d3chart.yAxis.axisLabel(chart.settings.get('y_axis_label'))
.axisLabelDistance(30);
-
+
// controls
d3chart.options({showControls: false});
-
+
// legend
if (d3chart.showLegend) {
d3chart.showLegend(chart.settings.get('show_legend') == 'true');
}
-
+
// make categories
self._makeAxes(d3chart, groups, chart.settings);
-
+
// custom callback
if (makeConfig) {
makeConfig(d3chart);
}
-
+
// hide controls if in multi-viewer mode
if (chart.settings.get('use_panels') === 'true') {
d3chart.options({showControls: false});
}
-
+
// hide min/max values
d3chart.xAxis.showMaxMin(false);
d3chart.yAxis.showMaxMin(chart.definition.showmaxmin);
-
+
+ // configure tooltips
+ d3chart.tooltipContent(function(key, x, y, graph) {
+ return '<h3>' + (graph.point.tooltip || key) + '</h3>';
+ });
+
// draw chart
if ($('#' + canvas_id).length == 0) {
return;
}
var canvas = d3.select('#' + canvas_id);
- canvas.datum(groups)
+ canvas.datum(groups)
.call(d3chart);
-
+
// add zoom/pan handler
if (chart.definition.zoomable && chart.definition.zoomable != 'native') {
// clip edges
if (d3chart.clipEdge) {
d3chart.clipEdge(true);
}
-
+
// add zoom
Tools.addZoom({
xAxis : d3chart.xAxis,
@@ -97,16 +102,16 @@
self._handleError(chart, err);
}
});
-
+
// return
return true;
},
-
+
// create axes formatting
_makeAxes: function(d3chart, groups, settings) {
// result
var categories = Tools.makeCategories(groups);
-
+
// make axes
function makeTickFormat (id) {
Tools.makeTickFormat({
@@ -125,7 +130,7 @@
makeTickFormat('x');
makeTickFormat('y');
},
-
+
// handle error
_handleError: function(chart, err) {
chart.state('failed', err);
diff -r 11d5bb0dd643c90472bebd5cc2b2d000c9ace85c -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
@@ -6,11 +6,11 @@
zoomable : true,
columns : {
x : {
- title : 'Values for x-axis',
+ title : 'Values for x-axis',
is_numeric : true
},
y : {
- title : 'Values for y-axis',
+ title : 'Values for y-axis',
is_numeric : true
}
}
diff -r 11d5bb0dd643c90472bebd5cc2b2d000c9ace85c -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 config/plugins/visualizations/charts/static/library/datasets.js
--- a/config/plugins/visualizations/charts/static/library/datasets.js
+++ b/config/plugins/visualizations/charts/static/library/datasets.js
@@ -299,7 +299,7 @@
// get/fix value
var v = column_data[j];
- if (isNaN(v) && !column.is_label) {
+ if (isNaN(v) && !column.is_label && !column.is_text) {
v = 0;
}
diff -r 11d5bb0dd643c90472bebd5cc2b2d000c9ace85c -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 config/plugins/visualizations/charts/static/views/group.js
--- a/config/plugins/visualizations/charts/static/views/group.js
+++ b/config/plugins/visualizations/charts/static/views/group.js
@@ -145,12 +145,13 @@
// link this
var self = this;
- // is a numeric number required
+ // available column options
var is_label = column_definition.is_label;
var is_auto = column_definition.is_auto;
var is_numeric = column_definition.is_numeric;
var is_unique = column_definition.is_unique;
var is_zero = column_definition.is_zero;
+ var is_text = column_definition.is_text;
// configure columns
var columns = [];
@@ -182,7 +183,7 @@
if (meta[key] == 'int' || meta[key] == 'float') {
valid = is_numeric;
} else {
- valid = is_label;
+ valid = is_text || is_label;
}
// check type
https://bitbucket.org/galaxy/galaxy-central/commits/b8fa3f9d0350/
Changeset: b8fa3f9d0350
User: arobinson
Date: 2015-02-17 18:21:03+00:00
Summary: Added Custom Authentication module support (CustomAuth)
Initial modules:
- ActiveDirectory (ldap)
- LocalDB (fall back to galaxy users)
- AlwaysAccept (whitelist)
- AlwaysReject (blacklist)
Sysadmin documentation at: https://docs.google.com/document/d/1CJp_m3vW7QKtAyBTMbE1MLgV6FAMuG3VO4HR-wH…
Testing documentation at: https://docs.google.com/document/d/1Cocx6Rt3eqPdm8IjOKYAR4RaY-9P2iFNXCt3AYg…
Affected #: 16 files
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 config/galaxy.ini.sample
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -844,6 +844,13 @@
#openid_config_file = config/openid_conf.xml
#openid_consumer_cache_path = database/openid_consumer_cache
+# Enable the use of custom authentication providers. Allows users to use their
+# Active Directory (or other) account instead of local authentication
+#enable_customauth = False
+#customauth_config_file = config/customauth_conf.xml
+# print debugging info for customauth
+#enable_customauth_echo = True
+
# Optional list of email addresses of API users who can make calls on behalf of
# other users
#api_allow_run_as = None
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -441,6 +441,10 @@
# Default chunk size for chunkable datatypes -- 64k
self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) )
+ # customauth
+ self.enable_customauth = string_as_bool( kwargs.get( 'enable_customauth', False ) )
+ self.customauth_config_file = resolve_path( kwargs.get( 'customauth_config_file', 'config/customauth_conf.xml' ), self.root )
+ self.enable_customauth_echo = string_as_bool( kwargs.get( 'enable_customauth_echo', False ) )
self.citation_cache_type = kwargs.get( "citation_cache_type", "file" )
self.citation_cache_data_dir = self.resolve_path( kwargs.get( "citation_cache_data_dir", "database/citations/data" ) )
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/customauth/__init__.py
--- /dev/null
+++ b/lib/galaxy/customauth/__init__.py
@@ -0,0 +1,208 @@
+'''
+Contains implementations of custom auth logic
+'''
+
+import traceback
+import xml.etree.ElementTree
+from yapsy.PluginManager import PluginManager
+
+from galaxy.security.validate_user_input import validate_publicname
+
+import logging
+logging.basicConfig(level=logging.DEBUG)
+
+# <customauth>
+# <authenticator>
+# <type>activedirectory</type>
+# <filter>'[username]'.endswith('@students.latrobe.edu.au')</filter>
+# <options>
+# <auto-register>True</auto-register>
+# <server>ldap://STUDENTS.ltu.edu.au</server>
+# [<search-filter>(&(objectClass=user)(mail={username}))</search-filter>
+# <search-base>dc=STUDENTS,dc=ltu,dc=edu,dc=au</search-base>
+# <search-user>jsmith</search-user>
+# <search-password>mysecret</search-password>
+# <search-fields>sAMAccountName</search-fields>]
+# <bind-user>{sAMAccountName}(a)STUDENTS.ltu.edu.au</bind-user>
+# <bind-password>{password}</bind-password>
+# <auto-register-username>{sAMAccountName}</auto-register-username>
+# </options>
+# </authenticator>
+# ...
+# </customauth>
+
+
+def check_registration_allowed(trans, email, password, configfile, debug=False):
+ '''Checks if the provided email is allowed to register.'''
+
+ message = ''
+ status = 'done'
+
+ for provider,options in activeAuthProviderGenerator(email, password, configfile, debug):
+ allowreg = _getTriState(options, 'allow-register', True)
+ if allowreg is None: # i.e. challenge
+ authresult, msg = provider.authenticate(email, password, options, debug)
+ if authresult == True:
+ break
+ if authresult is None:
+ message = 'Invalid email address or password'
+ status = 'error'
+ break
+ elif allowreg is True:
+ break
+ elif allowreg is False:
+ message = 'Account registration not required for your account. Please simply login.'
+ status = 'error'
+ break
+
+ return message, status
+
+
+def check_auto_registration(trans, email, password, configfile, debug=False):
+ '''Checks the email/password using custom auth providers and if matches returns
+ the 'auto-register' option for that provider'''
+
+ for provider,options in activeAuthProviderGenerator(email, password, configfile, debug):
+ if provider is None:
+ if debug:
+ print "Unable to find module: %s" % options
+ else:
+ authresult, autousername = provider.authenticate(email, password, options, debug)
+ autousername = str(autousername).lower()
+ if authresult is True:
+ # make username unique
+ if validate_publicname( trans, autousername ) != '':
+ i = 1
+ while i <= 10: # stop after 10 tries
+ if validate_publicname( trans, "%s-%i" % (autousername, i) ) == '':
+ autousername = "%s-%i" % (autousername, i)
+ break
+ i += 1
+ else:
+ break # end for loop if we can't make a unique username
+ if debug:
+ print "Email: %s, auto-register with username: %s" % (email, autousername)
+ return (_getBool(options, 'auto-register', False), autousername)
+ elif authresult is None:
+ print "Email: %s, stopping due to failed non-continue" % (email)
+ break # end authentication (skip rest)
+
+ return (False, '')
+
+
+def check_password(user, password, configfile, debug=False):
+ '''Checks the email/password using custom auth providers'''
+
+ if debug:
+ print ("Checking with CustomAuth")
+
+
+ for provider,options in activeAuthProviderGenerator(user.email, password, configfile, debug):
+ if provider is None:
+ if debug:
+ print "Unable to find module: %s" % options
+ else:
+ authresult = provider.authenticateUser(user, password, options, debug)
+ if authresult is True:
+ return True # accept user
+ elif authresult is None:
+ break # end authentication (skip rest)
+
+ return False
+
+def check_change_password(user, current_password, configfile, debug=False):
+ '''Checks that provider allows password changes and current_password matches'''
+
+ if debug:
+ print ("Checking password change with CustomAuth")
+
+ for provider,options in activeAuthProviderGenerator(user.email, current_password, configfile, debug):
+ if provider is None:
+ if debug:
+ print "Unable to find module: %s" % options
+ else:
+ if _getBool(options, "allow-password-change", False):
+ authresult = provider.authenticateUser(user, current_password, options, debug)
+ if authresult is True:
+ return (True, '') # accept user
+ elif authresult is None:
+ break # end authentication (skip rest)
+ else:
+ return (False, 'Password change not supported')
+ return (False, 'Invalid current password')
+
+
+
+def activeAuthProviderGenerator(username, password, configfile, debug):
+ '''Yields CustomAuthProvider instances for the provided configfile that match the filters'''
+
+ try:
+ # load the yapsy plugins
+ manager = PluginManager()
+ manager.setPluginPlaces(["lib/galaxy/customauth/providers"])
+ manager.collectPlugins()
+
+ if debug:
+ print ("Plugins found:")
+ for plugin in manager.getAllPlugins():
+ print ("- %s" % (plugin.path))
+
+ # parse XML
+ ct = xml.etree.ElementTree.parse(configfile)
+ confroot = ct.getroot()
+
+ # process authenticators
+ for authelem in confroot.getchildren():
+ typeelem = authelem.iter('type').next()
+
+ # check filterelem
+ filterelem = _getChildElement(authelem, 'filter')
+ if filterelem is not None:
+ filterstr = str(filterelem.text).format(username=username, password=password)
+ if debug:
+ print ("Filter: %s == %s" % (filterstr, eval(filterstr, {"__builtins__":None},{'str':str})))
+ if not eval(filterstr, {"__builtins__":None},{'str':str}):
+ continue # skip to next
+
+ # extract options
+ optionselem = _getChildElement(authelem, 'options')
+ options = {}
+ if optionselem is not None:
+ for opt in optionselem:
+ options[opt.tag] = opt.text
+
+ # get the instance
+ plugin = manager.getPluginByName(typeelem.text)
+ yield (plugin.plugin_object, options) # excepts if type is spelled incorrectly
+ except GeneratorExit:
+ return
+ except:
+ if debug:
+ print ('CustomAuth: Exception:\n%s' % (traceback.format_exc(),))
+
+
+def _getBool(d, k, o):
+ if k in d:
+ if d[k] in ('True', 'true', 'Yes', 'yes', '1', 1, True):
+ return True
+ else:
+ return False
+ else:
+ return o
+
+def _getTriState(d, k, o):
+ if k in d:
+ if d[k] in ('True', 'true', 'Yes', 'yes', '1', 1, True):
+ return True
+ elif d[k] in ('False', 'false', 'No', 'no', '0', 0, False):
+ return False
+ else:
+ return None
+ else:
+ return o
+
+def _getChildElement(parent, childname):
+ try:
+ return parent.iter(childname).next()
+ except StopIteration:
+ return None
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/customauth/base.py
--- /dev/null
+++ b/lib/galaxy/customauth/base.py
@@ -0,0 +1,41 @@
+'''
+Created on 15/07/2014
+
+@author: Andrew Robinson
+'''
+
+
+from yapsy.IPlugin import IPlugin
+
+class CustomAuthProvider(IPlugin):
+ '''A base class for all Custom Auth Providers'''
+
+ def authenticate(self, username, password, options, debug=False):
+ '''
+ Check the username and password are correct.
+
+ NOTE: Used within auto-registration to check its ok to register this user
+
+ @param username: the users email address
+ @param password: the plain text passord they typed
+ @param options: dictionary of options provided by admin in customauth xml config file
+ @param debug: boolean, False indicating admin wants debugging information printed
+ @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
+ '''
+
+ return False
+
+ def authenticateUser(self, user, password, options, debug=False):
+ '''
+ Same as authenticate, except User object is provided instead of username.
+
+ NOTE: used on normal login to check authentication and update user details if required.
+
+ @param username: the users email address
+ @param password: the plain text passord they typed
+ @param options: dictionary of options provided by admin in customauth xml config file
+ @param debug: boolean, False indicating admin wants debugging information printed
+ @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
+ '''
+
+ return False
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/customauth/providers/activedirectory.py
--- /dev/null
+++ b/lib/galaxy/customauth/providers/activedirectory.py
@@ -0,0 +1,119 @@
+'''
+Created on 15/07/2014
+
+@author: Andrew Robinson
+'''
+
+import traceback
+import galaxy.customauth.base
+
+
+def _getsubs(d, k, vars, default=''):
+ if k in d:
+ return str(d[k]).format(**vars)
+ return str(default).format(**vars)
+
+def _getopt(d, k, default):
+ if k in d:
+ return d[k]
+ return default
+
+class ActiveDirectory(galaxy.customauth.base.CustomAuthProvider):
+ '''
+ Attempts to authenticate them against the Active directory
+
+ If options include search-fields then it will attempt to search the AD for
+ those fields first. After that it will bind to the AD with the username
+ (formatted as specified)
+ '''
+
+ def authenticate(self, username, password, options, debug=False):
+ '''
+ Check the username and password are correct.
+
+ NOTE: Used within auto-registration to check its ok to register this user
+
+ @param username: the users email address
+ @param password: the plain text passord they typed
+ @param options: dictionary of options provided by admin in customauth xml config file
+ @param debug: boolean, False indicating admin wants debugging information printed
+ @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
+ '''
+
+ if debug:
+ print ("Username: %s" % username)
+ print ("Options: %s" % options)
+
+ failuremode = False # reject but continue
+ if _getopt(options, 'continue-on-failure', 'False') == 'False':
+ failuremode = None # reject and do not continue
+
+ try:
+ import ldap
+ except:
+ if debug:
+ print ("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
+ return (failuremode, '')
+
+ ## do AD search (if required) ##
+ vars = {'username': username, 'password': password}
+ if 'search-fields' in options:
+ try:
+ # setup connection
+ ldap.set_option(ldap.OPT_REFERRALS, 0)
+ l = ldap.initialize(_getsubs(options,'server',vars))
+ l.protocol_version = 3
+ l.simple_bind_s(_getsubs(options,'search-user',vars), _getsubs(options,'search-password',vars))
+ scope = ldap.SCOPE_SUBTREE
+
+ # setup search
+ attributes = map(lambda s: s.strip().format(**vars), options['search-fields'].split(','))
+ result = l.search(_getsubs(options,'search-base',vars), scope, _getsubs(options,'search-filter',vars), attributes)
+
+ # parse results
+ _,suser = l.result(result,60)
+ _,attrs = suser[0]
+ if debug:
+ print ("AD Search attributes: %s" % attrs)
+ if hasattr(attrs, 'has_key'):
+ for attr in attributes:
+ if attrs.has_key(attr):
+ vars[attr] = str(attrs[attr][0])
+ else:
+ vars[attr] = ""
+ except Exception:
+ if debug:
+ print('User: %s, ACTIVEDIRECTORY: Search Exception:\n%s' % (username, traceback.format_exc(),))
+ return (failuremode, '')
+ # end search
+
+ # bind as user to check their credentials
+ try:
+ # setup connection
+ ldap.set_option(ldap.OPT_REFERRALS, 0)
+ l = ldap.initialize(_getsubs(options,'server',vars))
+ l.protocol_version = 3
+ l.simple_bind_s(_getsubs(options,'bind-user',vars), _getsubs(options,'bind-password',vars))
+ except Exception:
+ if debug:
+ print('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc(),))
+ return (failuremode, '')
+
+ if debug:
+ print "User: %s, ACTIVEDIRECTORY: True" % (username)
+ return (True, _getsubs(options,'auto-register-username',vars))
+
+ def authenticateUser(self, user, password, options, debug=False):
+ '''
+ Same as authenticate, except User object is provided instead of username.
+
+ NOTE: used on normal login to check authentication and update user details if required.
+
+ @param username: the users email address
+ @param password: the plain text passord they typed
+ @param options: dictionary of options provided by admin in customauth xml config file
+ @param debug: boolean, False indicating admin wants debugging information printed
+ @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
+ '''
+
+ return self.authenticate(user.email, password, options, debug)[0]
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/customauth/providers/activedirectory.yapsy-plugin
--- /dev/null
+++ b/lib/galaxy/customauth/providers/activedirectory.yapsy-plugin
@@ -0,0 +1,8 @@
+[Core]
+Name = ActiveDirectory
+Module = activedirectory
+
+[Documentation]
+Author = Andrew Robinson
+Version = 0.1
+Description = Custom Authentication Provider that authenticates against an ActiveDirectory (via LDAP). Requires python-ldap module.
\ No newline at end of file
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/customauth/providers/alwaysaccept.py
--- /dev/null
+++ b/lib/galaxy/customauth/providers/alwaysaccept.py
@@ -0,0 +1,49 @@
+'''
+Created on 16/07/2014
+
+@author: Andrew Robinson
+'''
+
+import traceback, re, string
+import galaxy.customauth.base
+
+
+class AlwaysAccept(galaxy.customauth.base.CustomAuthProvider):
+ '''A simple authenticator that just accepts user (doesn't care about their password)'''
+
+ def authenticate(self, username, password, options, debug=False):
+ '''
+ Check the username and password are correct.
+
+ NOTE: Used within auto-registration to check its ok to register this user
+
+ @param username: the users email address
+ @param password: the plain text passord they typed
+ @param options: dictionary of options provided by admin in customauth xml config file
+ @param debug: boolean, False indicating admin wants debugging information printed
+ @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
+ '''
+ if debug:
+ print ("User: %s, ALWAYSACCEPT: True (%s)" % (username, _stripUsername(username)))
+ return (True, _stripUsername(username))
+
+ def authenticateUser(self, user, password, options, debug=False):
+ '''
+ Same as authenticate, except User object is provided instead of username.
+
+ NOTE: used on normal login to check authentication and update user details if required.
+
+ @param username: the users email address
+ @param password: the plain text passord they typed
+ @param options: dictionary of options provided by admin in customauth xml config file
+ @param debug: boolean, False indicating admin wants debugging information printed
+ @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
+ '''
+
+ if debug:
+ print ("User: %s, ALWAYSACCEPT: True" % (user.email))
+ return True
+
+def _stripUsername(username):
+ pattern = re.compile('[^a-zA-Z0-9\-]+')
+ return pattern.sub("-", username)
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/customauth/providers/alwaysaccept.yapsy-plugin
--- /dev/null
+++ b/lib/galaxy/customauth/providers/alwaysaccept.yapsy-plugin
@@ -0,0 +1,8 @@
+[Core]
+Name = AlwaysAccept
+Module = alwaysaccept
+
+[Documentation]
+Author = Andrew Robinson
+Version = 0.1
+Description = Custom Authentication Provider that is used for whitelisting usernames (i.e. accept any password)
\ No newline at end of file
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/customauth/providers/alwaysreject.py
--- /dev/null
+++ b/lib/galaxy/customauth/providers/alwaysreject.py
@@ -0,0 +1,42 @@
+'''
+Created on 16/07/2014
+
+@author: Andrew Robinson
+'''
+
+import traceback
+import galaxy.customauth.base
+
+class AlwaysReject(galaxy.customauth.base.CustomAuthProvider):
+ '''A simple authenticator that just accepts user (doesn't care about their password)'''
+
+ def authenticate(self, username, password, options, debug=False):
+ '''
+ Check the username and password are correct.
+
+ NOTE: Used within auto-registration to check its ok to register this user
+
+ @param username: the users email address
+ @param password: the plain text passord they typed
+ @param options: dictionary of options provided by admin in customauth xml config file
+ @param debug: boolean, False indicating admin wants debugging information printed
+ @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
+ '''
+ return (None, '')
+
+ def authenticateUser(self, user, password, options, debug=False):
+ '''
+ Same as authenticate, except User object is provided instead of username.
+
+ NOTE: used on normal login to check authentication and update user details if required.
+
+ @param username: the users email address
+ @param password: the plain text passord they typed
+ @param options: dictionary of options provided by admin in customauth xml config file
+ @param debug: boolean, False indicating admin wants debugging information printed
+ @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
+ '''
+
+ if debug:
+ print ("User: %s, ALWAYSREJECT: None" % (user.email))
+ return None
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/customauth/providers/alwaysreject.yapsy-plugin
--- /dev/null
+++ b/lib/galaxy/customauth/providers/alwaysreject.yapsy-plugin
@@ -0,0 +1,8 @@
+[Core]
+Name = AlwaysReject
+Module = alwaysreject
+
+[Documentation]
+Author = Andrew Robinson
+Version = 0.1
+Description = Custom Authentication Provider that is used for blacklisting usernames (i.e. accept no password)
\ No newline at end of file
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/customauth/providers/localdb.py
--- /dev/null
+++ b/lib/galaxy/customauth/providers/localdb.py
@@ -0,0 +1,44 @@
+'''
+Created on 16/07/2014
+
+@author: Andrew Robinson
+'''
+
+import traceback
+import galaxy.customauth.base
+
+class LocalDB(galaxy.customauth.base.CustomAuthProvider):
+ '''Checks against local DB (as per usual)'''
+
+ def authenticate(self, username, password, options, debug=False):
+ '''
+ Check the username and password are correct.
+
+ NOTE: Used within auto-registration to check its ok to register this user
+
+ @param username: the users email address
+ @param password: the plain text passord they typed
+ @param options: dictionary of options provided by admin in customauth xml config file
+ @param debug: boolean, False indicating admin wants debugging information printed
+ @return: (boolean, str), True: accept user, False: reject user and None: reject user and don't try any other providers. str is the username to register with if accepting.
+ '''
+
+ return (False, '') # it can never auto-create based of localdb (chicken-egg)
+
+ def authenticateUser(self, user, password, options, debug=False):
+ '''
+ Same as authenticate, except User object is provided instead of username.
+
+ NOTE: used on normal login to check authentication and update user details if required.
+
+ @param username: the users email address
+ @param password: the plain text passord they typed
+ @param options: dictionary of options provided by admin in customauth xml config file
+ @param debug: boolean, False indicating admin wants debugging information printed
+ @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
+ '''
+
+ user_ok = user.check_password(password)
+ if debug:
+ print ("User: %s, LOCALDB: %s" % (user.email, user_ok))
+ return user_ok
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/customauth/providers/localdb.yapsy-plugin
--- /dev/null
+++ b/lib/galaxy/customauth/providers/localdb.yapsy-plugin
@@ -0,0 +1,8 @@
+[Core]
+Name = LocalDB
+Module = localdb
+
+[Documentation]
+Author = Andrew Robinson
+Version = 0.1
+Description = Custom Authentication Provider that checks against the local database as per normal.
\ No newline at end of file
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/webapps/galaxy/api/authenticate.py
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -18,6 +18,7 @@
from galaxy.managers import api_keys
from galaxy import exceptions
from galaxy.web.base.controller import BaseAPIController
+import galaxy.customauth
import logging
log = logging.getLogger( __name__ )
@@ -52,7 +53,10 @@
raise exceptions.InconsistentDatabase( 'An error occured, please contact your administrator.' )
else:
user = user[0]
- is_valid_user = user.check_password( password )
+ if (trans.app.config.enable_customauth):
+ is_valid_user = galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo)
+ else:
+ is_valid_user = user.check_password( password )
if ( is_valid_user ):
key = self.api_keys_manager.get_or_create_api_key( user )
return dict( api_key=key )
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/webapps/galaxy/controllers/mobile.py
--- a/lib/galaxy/webapps/galaxy/controllers/mobile.py
+++ b/lib/galaxy/webapps/galaxy/controllers/mobile.py
@@ -1,6 +1,7 @@
from galaxy import web
from galaxy.web.base.controller import *
+import galaxy.customauth
class Mobile( BaseUIController ):
@@ -58,12 +59,35 @@
# error = password_error = None
# user = trans.sa_session.query( model.User ).filter_by( email = email ).first()
# if not user:
- # error = "No such user (please note that login is case sensitive)"
+ # if trans.app.config.enable_customauth:
+ # autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo)
+ # if autoreg[0]:
+ # kwd = {}
+ # kwd['username'] = autoreg[1]
+ # params = util.Params( kwd )
+ # message = validate_email( trans, email )
+ # if not message:
+ # message, status, user, success = self.__register( trans, 'user', False, **kwd )
+ # if success:
+ # The handle_user_login() method has a call to the history_set_default_permissions() method
+ # (needed when logging in with a history), user needs to have default permissions set before logging in
+ # trans.handle_user_login( user )
+ # trans.log_event( "User (auto) created a new account" )
+ # trans.log_event( "User logged in" )
+ # else:
+ # message = "Auto-registration failed, contact your local Galaxy administrator. %s" %message
+ # else:
+ # message = "Auto-registration failed, contact your local Galaxy administrator. %s" %message
+ # else:
+ # message = "No such user (please note that login is case sensitive)"
+ # else:
+ # message = "No such user (please note that login is case sensitive)"
# elif user.deleted:
# error = "This account has been marked deleted, contact your Galaxy administrator to restore the account."
# elif user.external:
# error = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it."
- # elif not user.check_password( password ):
+ # elif not trans.app.config.enable_customauth and not user.check_password( password ) or \
+ # trans.app.config.enable_customauth and not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo):
# error = "Invalid password"
# else:
# trans.handle_user_login( user )
diff -r 56e108003f4eb1d35ea304ebdd3240c0508a91c4 -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -28,6 +28,7 @@
UsesFormDefinitionsMixin)
from galaxy.web.form_builder import build_select_field, CheckboxField
from galaxy.web.framework.helpers import escape, grids, time_ago
+import galaxy.customauth
log = logging.getLogger( __name__ )
@@ -513,8 +514,33 @@
redirect = kwd.get( 'redirect', trans.request.referer ).strip()
success = False
user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first()
+ if trans.app.config.enable_customauth_echo:
+ print ("trans.app.config.enable_customauth: %s" % trans.app.config.enable_customauth)
+ print ("trans.app.config.customauth_config_file: %s" % trans.app.config.customauth_config_file)
+ print ("trans.app.config.enable_customauth_echo: %s WARNING: don't use in production" % trans.app.config.enable_customauth_echo)
if not user:
- message = "No such user (please note that login is case sensitive)"
+ if trans.app.config.enable_customauth:
+ autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo)
+ if autoreg[0]:
+ kwd['username'] = autoreg[1]
+ params = util.Params( kwd )
+ message = validate_email( trans, email ) #self.__validate( trans, params, email, password, password, username )
+ if not message:
+ message, status, user, success = self.__register( trans, 'user', False, **kwd )
+ if success:
+ # The handle_user_login() method has a call to the history_set_default_permissions() method
+ # (needed when logging in with a history), user needs to have default permissions set before logging in
+ trans.handle_user_login( user )
+ trans.log_event( "User (auto) created a new account" )
+ trans.log_event( "User logged in" )
+ else:
+ message = "Auto-registration failed, contact your local Galaxy administrator. %s" %message
+ else:
+ message = "Auto-registration failed, contact your local Galaxy administrator. %s" %message
+ else:
+ message = "No such user or invalid password"
+ else:
+ message = "No such user (please note that login is case sensitive)"
elif user.deleted:
message = "This account has been marked deleted, contact your local Galaxy administrator to restore the account."
if trans.app.config.error_email_to is not None:
@@ -523,7 +549,8 @@
message = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it."
if trans.app.config.error_email_to is not None:
message += ' Contact: %s' % trans.app.config.error_email_to
- elif not user.check_password( password ):
+ elif not trans.app.config.enable_customauth and not user.check_password( password ) or \
+ trans.app.config.enable_customauth and not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo):
message = "Invalid password"
elif trans.app.config.user_activation_on and not user.active: # activation is ON and the user is INACTIVE
if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON
@@ -651,41 +678,46 @@
message += ' Contact: %s' % trans.app.config.error_email_to
status = 'error'
else:
- if not refresh_frames:
- if trans.webapp.name == 'galaxy':
- if trans.app.config.require_login:
- refresh_frames = [ 'masthead', 'history', 'tools' ]
+ # check user is allowed to register
+ message = ''
+ if trans.app.config.enable_customauth:
+ message, status = galaxy.customauth.check_registration_allowed(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo)
+ if message == '':
+ if not refresh_frames:
+ if trans.webapp.name == 'galaxy':
+ if trans.app.config.require_login:
+ refresh_frames = [ 'masthead', 'history', 'tools' ]
+ else:
+ refresh_frames = [ 'masthead', 'history' ]
else:
- refresh_frames = [ 'masthead', 'history' ]
- else:
- refresh_frames = [ 'masthead' ]
- # Create the user, save all the user info and login to Galaxy
- if params.get( 'create_user_button', False ):
- # Check email and password validity
- message = self.__validate( trans, params, email, password, confirm, username )
- if not message:
- # All the values are valid
- message, status, user, success = self.__register( trans,
- cntrller,
- subscribe_checked,
- **kwd )
- if trans.webapp.name == 'tool_shed':
- redirect_url = url_for( '/' )
- if success and not is_admin:
- # The handle_user_login() method has a call to the history_set_default_permissions() method
- # (needed when logging in with a history), user needs to have default permissions set before logging in
- trans.handle_user_login( user )
- trans.log_event( "User created a new account" )
- trans.log_event( "User logged in" )
- if success and is_admin:
- message = 'Created new user account (%s)' % escape( user.email )
- trans.response.send_redirect( web.url_for( controller='admin',
- action='users',
- cntrller=cntrller,
- message=message,
- status=status ) )
- else:
- status = 'error'
+ refresh_frames = [ 'masthead' ]
+ # Create the user, save all the user info and login to Galaxy
+ if params.get( 'create_user_button', False ):
+ # Check email and password validity
+ message = self.__validate( trans, params, email, password, confirm, username )
+ if not message:
+ # All the values are valid
+ message, status, user, success = self.__register( trans,
+ cntrller,
+ subscribe_checked,
+ **kwd )
+ if trans.webapp.name == 'tool_shed':
+ redirect_url = url_for( '/' )
+ if success and not is_admin:
+ # The handle_user_login() method has a call to the history_set_default_permissions() method
+ # (needed when logging in with a history), user needs to have default permissions set before logging in
+ trans.handle_user_login( user )
+ trans.log_event( "User created a new account" )
+ trans.log_event( "User logged in" )
+ if success and is_admin:
+ message = 'Created new user account (%s)' % escape( user.email )
+ trans.response.send_redirect( web.url_for( controller='admin',
+ action='users',
+ cntrller=cntrller,
+ message=message,
+ status=status ) )
+ else:
+ status = 'error'
if trans.webapp.name == 'galaxy':
user_type_form_definition = self.__get_user_type_form_definition( trans, user=None, **kwd )
user_type_fd_id = params.get( 'user_type_fd_id', 'none' )
@@ -1100,7 +1132,13 @@
return trans.show_error_message("Invalid or expired password reset token, please request a new one.")
else:
# The user is changing their own password, validate their current password
- if trans.user.check_password( current ):
+ if trans.app.config.enable_customauth:
+ (ok, message) = galaxy.customauth.check_change_password(trans.user, current, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo)
+ if ok:
+ user = trans.user
+ else:
+ status = "error"
+ elif trans.user.check_password( current ):
user = trans.user
else:
message = 'Invalid current password'
https://bitbucket.org/galaxy/galaxy-central/commits/29d484334434/
Changeset: 29d484334434
User: nsoranzo
Date: 2015-02-17 18:34:32+00:00
Summary: Rename enable_customauth_echo config option to customauth_debug.
Affected #: 5 files
diff -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 -r 29d48433443418575d112e9aa21e4f4669d861a5 config/galaxy.ini.sample
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -845,14 +845,14 @@
#openid_consumer_cache_path = database/openid_consumer_cache
# Enable the use of custom authentication providers. Allows users to use their
-# Active Directory (or other) account instead of local authentication
+# Active Directory (or other) account instead of local authentication.
#enable_customauth = False
#customauth_config_file = config/customauth_conf.xml
-# print debugging info for customauth
-#enable_customauth_echo = True
+# Print debugging info for customauth
+#customauth_debug = False
# Optional list of email addresses of API users who can make calls on behalf of
-# other users
+# other users.
#api_allow_run_as = None
# Master key that allows many API admin actions to be used without actually
diff -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 -r 29d48433443418575d112e9aa21e4f4669d861a5 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -444,7 +444,7 @@
# customauth
self.enable_customauth = string_as_bool( kwargs.get( 'enable_customauth', False ) )
self.customauth_config_file = resolve_path( kwargs.get( 'customauth_config_file', 'config/customauth_conf.xml' ), self.root )
- self.enable_customauth_echo = string_as_bool( kwargs.get( 'enable_customauth_echo', False ) )
+ self.customauth_debug = string_as_bool( kwargs.get( 'customauth_debug', False ) )
self.citation_cache_type = kwargs.get( "citation_cache_type", "file" )
self.citation_cache_data_dir = self.resolve_path( kwargs.get( "citation_cache_data_dir", "database/citations/data" ) )
diff -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 -r 29d48433443418575d112e9aa21e4f4669d861a5 lib/galaxy/webapps/galaxy/api/authenticate.py
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -54,7 +54,7 @@
else:
user = user[0]
if (trans.app.config.enable_customauth):
- is_valid_user = galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo)
+ is_valid_user = galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
else:
is_valid_user = user.check_password( password )
if ( is_valid_user ):
diff -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 -r 29d48433443418575d112e9aa21e4f4669d861a5 lib/galaxy/webapps/galaxy/controllers/mobile.py
--- a/lib/galaxy/webapps/galaxy/controllers/mobile.py
+++ b/lib/galaxy/webapps/galaxy/controllers/mobile.py
@@ -60,7 +60,7 @@
# user = trans.sa_session.query( model.User ).filter_by( email = email ).first()
# if not user:
# if trans.app.config.enable_customauth:
- # autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo)
+ # autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
# if autoreg[0]:
# kwd = {}
# kwd['username'] = autoreg[1]
@@ -87,7 +87,7 @@
# elif user.external:
# error = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it."
# elif not trans.app.config.enable_customauth and not user.check_password( password ) or \
- # trans.app.config.enable_customauth and not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo):
+ # trans.app.config.enable_customauth and not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug):
# error = "Invalid password"
# else:
# trans.handle_user_login( user )
diff -r b8fa3f9d03500f83704e792e769e6be1f9c4a077 -r 29d48433443418575d112e9aa21e4f4669d861a5 lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -514,13 +514,13 @@
redirect = kwd.get( 'redirect', trans.request.referer ).strip()
success = False
user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first()
- if trans.app.config.enable_customauth_echo:
+ if trans.app.config.customauth_debug:
print ("trans.app.config.enable_customauth: %s" % trans.app.config.enable_customauth)
print ("trans.app.config.customauth_config_file: %s" % trans.app.config.customauth_config_file)
- print ("trans.app.config.enable_customauth_echo: %s WARNING: don't use in production" % trans.app.config.enable_customauth_echo)
+ print ("trans.app.config.customauth_debug: %s WARNING: don't use in production" % trans.app.config.customauth_debug)
if not user:
if trans.app.config.enable_customauth:
- autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo)
+ autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
if autoreg[0]:
kwd['username'] = autoreg[1]
params = util.Params( kwd )
@@ -550,7 +550,7 @@
if trans.app.config.error_email_to is not None:
message += ' Contact: %s' % trans.app.config.error_email_to
elif not trans.app.config.enable_customauth and not user.check_password( password ) or \
- trans.app.config.enable_customauth and not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo):
+ trans.app.config.enable_customauth and not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug):
message = "Invalid password"
elif trans.app.config.user_activation_on and not user.active: # activation is ON and the user is INACTIVE
if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON
@@ -681,7 +681,7 @@
# check user is allowed to register
message = ''
if trans.app.config.enable_customauth:
- message, status = galaxy.customauth.check_registration_allowed(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo)
+ message, status = galaxy.customauth.check_registration_allowed(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
if message == '':
if not refresh_frames:
if trans.webapp.name == 'galaxy':
@@ -1133,7 +1133,7 @@
else:
# The user is changing their own password, validate their current password
if trans.app.config.enable_customauth:
- (ok, message) = galaxy.customauth.check_change_password(trans.user, current, trans.app.config.customauth_config_file, trans.app.config.enable_customauth_echo)
+ (ok, message) = galaxy.customauth.check_change_password(trans.user, current, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
if ok:
user = trans.user
else:
https://bitbucket.org/galaxy/galaxy-central/commits/8ae0eb0b5567/
Changeset: 8ae0eb0b5567
User: nsoranzo
Date: 2015-02-17 19:10:11+00:00
Summary: Remove AlwaysAccept customauth plugin.
Affected #: 2 files
diff -r 29d48433443418575d112e9aa21e4f4669d861a5 -r 8ae0eb0b556790796c2da2477db0fcd777ae13a7 lib/galaxy/customauth/providers/alwaysaccept.py
--- a/lib/galaxy/customauth/providers/alwaysaccept.py
+++ /dev/null
@@ -1,49 +0,0 @@
-'''
-Created on 16/07/2014
-
-@author: Andrew Robinson
-'''
-
-import traceback, re, string
-import galaxy.customauth.base
-
-
-class AlwaysAccept(galaxy.customauth.base.CustomAuthProvider):
- '''A simple authenticator that just accepts user (doesn't care about their password)'''
-
- def authenticate(self, username, password, options, debug=False):
- '''
- Check the username and password are correct.
-
- NOTE: Used within auto-registration to check its ok to register this user
-
- @param username: the users email address
- @param password: the plain text passord they typed
- @param options: dictionary of options provided by admin in customauth xml config file
- @param debug: boolean, False indicating admin wants debugging information printed
- @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
- '''
- if debug:
- print ("User: %s, ALWAYSACCEPT: True (%s)" % (username, _stripUsername(username)))
- return (True, _stripUsername(username))
-
- def authenticateUser(self, user, password, options, debug=False):
- '''
- Same as authenticate, except User object is provided instead of username.
-
- NOTE: used on normal login to check authentication and update user details if required.
-
- @param username: the users email address
- @param password: the plain text passord they typed
- @param options: dictionary of options provided by admin in customauth xml config file
- @param debug: boolean, False indicating admin wants debugging information printed
- @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
- '''
-
- if debug:
- print ("User: %s, ALWAYSACCEPT: True" % (user.email))
- return True
-
-def _stripUsername(username):
- pattern = re.compile('[^a-zA-Z0-9\-]+')
- return pattern.sub("-", username)
diff -r 29d48433443418575d112e9aa21e4f4669d861a5 -r 8ae0eb0b556790796c2da2477db0fcd777ae13a7 lib/galaxy/customauth/providers/alwaysaccept.yapsy-plugin
--- a/lib/galaxy/customauth/providers/alwaysaccept.yapsy-plugin
+++ /dev/null
@@ -1,8 +0,0 @@
-[Core]
-Name = AlwaysAccept
-Module = alwaysaccept
-
-[Documentation]
-Author = Andrew Robinson
-Version = 0.1
-Description = Custom Authentication Provider that is used for whitelisting usernames (i.e. accept any password)
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/5ae99e242774/
Changeset: 5ae99e242774
User: nsoranzo
Date: 2015-02-17 19:50:30+00:00
Summary: PEP-8, doc and other fixes suggested in PR #555 review.
Affected #: 7 files
diff -r 8ae0eb0b556790796c2da2477db0fcd777ae13a7 -r 5ae99e2427746abb436eb82231372c69a61017e0 lib/galaxy/customauth/__init__.py
--- a/lib/galaxy/customauth/__init__.py
+++ b/lib/galaxy/customauth/__init__.py
@@ -1,6 +1,6 @@
-'''
-Contains implementations of custom auth logic
-'''
+"""
+Contains implementations of custom auth logic.
+"""
import traceback
import xml.etree.ElementTree
@@ -31,14 +31,11 @@
# ...
# </customauth>
-
-def check_registration_allowed(trans, email, password, configfile, debug=False):
- '''Checks if the provided email is allowed to register.'''
-
+def check_registration_allowed(email, password, configfile, debug=False):
+ """Checks if the provided email is allowed to register."""
message = ''
status = 'done'
-
- for provider,options in activeAuthProviderGenerator(email, password, configfile, debug):
+ for provider, options in activeAuthProviderGenerator(email, password, configfile, debug):
allowreg = _getTriState(options, 'allow-register', True)
if allowreg is None: # i.e. challenge
authresult, msg = provider.authenticate(email, password, options, debug)
@@ -54,15 +51,13 @@
message = 'Account registration not required for your account. Please simply login.'
status = 'error'
break
-
return message, status
-
def check_auto_registration(trans, email, password, configfile, debug=False):
- '''Checks the email/password using custom auth providers and if matches returns
- the 'auto-register' option for that provider'''
-
- for provider,options in activeAuthProviderGenerator(email, password, configfile, debug):
+ """Checks the email/password using custom auth providers and if matches
+ returns the 'auto-register' option for that provider.
+ """
+ for provider, options in activeAuthProviderGenerator(email, password, configfile, debug):
if provider is None:
if debug:
print "Unable to find module: %s" % options
@@ -86,18 +81,14 @@
elif authresult is None:
print "Email: %s, stopping due to failed non-continue" % (email)
break # end authentication (skip rest)
-
return (False, '')
-
def check_password(user, password, configfile, debug=False):
- '''Checks the email/password using custom auth providers'''
-
+ """Checks the email/password using custom auth providers."""
if debug:
print ("Checking with CustomAuth")
-
-
- for provider,options in activeAuthProviderGenerator(user.email, password, configfile, debug):
+
+ for provider, options in activeAuthProviderGenerator(user.email, password, configfile, debug):
if provider is None:
if debug:
print "Unable to find module: %s" % options
@@ -107,16 +98,15 @@
return True # accept user
elif authresult is None:
break # end authentication (skip rest)
-
return False
def check_change_password(user, current_password, configfile, debug=False):
- '''Checks that provider allows password changes and current_password matches'''
-
+ """Checks that provider allows password changes and current_password
+ matches.
+ """
if debug:
print ("Checking password change with CustomAuth")
-
- for provider,options in activeAuthProviderGenerator(user.email, current_password, configfile, debug):
+ for provider, options in activeAuthProviderGenerator(user.email, current_password, configfile, debug):
if provider is None:
if debug:
print "Unable to find module: %s" % options
@@ -130,31 +120,30 @@
else:
return (False, 'Password change not supported')
return (False, 'Invalid current password')
-
-
def activeAuthProviderGenerator(username, password, configfile, debug):
- '''Yields CustomAuthProvider instances for the provided configfile that match the filters'''
-
+ """Yields CustomAuthProvider instances for the provided configfile that
+ match the filters.
+ """
try:
# load the yapsy plugins
manager = PluginManager()
- manager.setPluginPlaces(["lib/galaxy/customauth/providers"])
+ manager.setPluginPlaces(["lib/galaxy/customauth/providers"])
manager.collectPlugins()
-
+
if debug:
print ("Plugins found:")
for plugin in manager.getAllPlugins():
print ("- %s" % (plugin.path))
-
+
# parse XML
ct = xml.etree.ElementTree.parse(configfile)
confroot = ct.getroot()
-
+
# process authenticators
for authelem in confroot.getchildren():
typeelem = authelem.iter('type').next()
-
+
# check filterelem
filterelem = _getChildElement(authelem, 'filter')
if filterelem is not None:
@@ -163,14 +152,14 @@
print ("Filter: %s == %s" % (filterstr, eval(filterstr, {"__builtins__":None},{'str':str})))
if not eval(filterstr, {"__builtins__":None},{'str':str}):
continue # skip to next
-
+
# extract options
optionselem = _getChildElement(authelem, 'options')
options = {}
if optionselem is not None:
for opt in optionselem:
options[opt.tag] = opt.text
-
+
# get the instance
plugin = manager.getPluginByName(typeelem.text)
yield (plugin.plugin_object, options) # excepts if type is spelled incorrectly
@@ -180,7 +169,6 @@
if debug:
print ('CustomAuth: Exception:\n%s' % (traceback.format_exc(),))
-
def _getBool(d, k, o):
if k in d:
if d[k] in ('True', 'true', 'Yes', 'yes', '1', 1, True):
@@ -189,7 +177,7 @@
return False
else:
return o
-
+
def _getTriState(d, k, o):
if k in d:
if d[k] in ('True', 'true', 'Yes', 'yes', '1', 1, True):
diff -r 8ae0eb0b556790796c2da2477db0fcd777ae13a7 -r 5ae99e2427746abb436eb82231372c69a61017e0 lib/galaxy/customauth/base.py
--- a/lib/galaxy/customauth/base.py
+++ b/lib/galaxy/customauth/base.py
@@ -1,41 +1,54 @@
-'''
+"""
Created on 15/07/2014
@author: Andrew Robinson
-'''
-
+"""
from yapsy.IPlugin import IPlugin
class CustomAuthProvider(IPlugin):
- '''A base class for all Custom Auth Providers'''
-
+ """A base class for all Custom Auth Providers."""
+
def authenticate(self, username, password, options, debug=False):
- '''
- Check the username and password are correct.
-
- NOTE: Used within auto-registration to check its ok to register this user
-
- @param username: the users email address
- @param password: the plain text passord they typed
- @param options: dictionary of options provided by admin in customauth xml config file
- @param debug: boolean, False indicating admin wants debugging information printed
- @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
- '''
-
- return False
-
+ """
+ Check that the username and password are correct.
+
+ NOTE: Used within auto-registration to check it is ok to register this
+ user.
+
+ :param username: the users email address
+ :type username: str
+ :param password: the plain text password they typed
+ :type password: str
+ :param options: options provided in customauth XML config file
+ :type options: dict
+ :param debug: whether to print debugging info (defaults to False)
+ :type debug: bool
+ :returns: True: accept user, False: reject user and None: reject user
+ and don't try any other providers. str is the username to register
+ with if accepting
+ :rtype: (bool, str)
+ """
+ raise NotImplementedError()
+
def authenticateUser(self, user, password, options, debug=False):
- '''
- Same as authenticate, except User object is provided instead of username.
-
- NOTE: used on normal login to check authentication and update user details if required.
-
- @param username: the users email address
- @param password: the plain text passord they typed
- @param options: dictionary of options provided by admin in customauth xml config file
- @param debug: boolean, False indicating admin wants debugging information printed
- @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
- '''
-
- return False
+ """
+ Same as authenticate() method, except an User object is provided instead
+ of a username.
+
+ NOTE: used on normal login to check authentication and update user
+ details if required.
+
+ :param username: the users email address
+ :type username: str
+ :param password: the plain text password they typed
+ :type password: str
+ :param options: options provided in customauth XML config file
+ :type options: dict
+ :param debug: whether to print debugging info (defaults to False)
+ :type debug: bool
+ :returns: True: accept user, False: reject user and None: reject user
+ and don't try any other providers
+ :rtype: bool
+ """
+ raise NotImplementedError()
diff -r 8ae0eb0b556790796c2da2477db0fcd777ae13a7 -r 5ae99e2427746abb436eb82231372c69a61017e0 lib/galaxy/customauth/providers/activedirectory.py
--- a/lib/galaxy/customauth/providers/activedirectory.py
+++ b/lib/galaxy/customauth/providers/activedirectory.py
@@ -1,8 +1,8 @@
-'''
+"""
Created on 15/07/2014
@author: Andrew Robinson
-'''
+"""
import traceback
import galaxy.customauth.base
@@ -13,48 +13,35 @@
return str(d[k]).format(**vars)
return str(default).format(**vars)
-def _getopt(d, k, default):
- if k in d:
- return d[k]
- return default
class ActiveDirectory(galaxy.customauth.base.CustomAuthProvider):
- '''
- Attempts to authenticate them against the Active directory
-
- If options include search-fields then it will attempt to search the AD for
- those fields first. After that it will bind to the AD with the username
- (formatted as specified)
- '''
-
+ """
+ Attempts to authenticate users against an Active Directory server.
+
+ If options include search-fields then it will attempt to search the AD for
+ those fields first. After that it will bind to the AD with the username
+ (formatted as specified).
+ """
+
def authenticate(self, username, password, options, debug=False):
- '''
- Check the username and password are correct.
-
- NOTE: Used within auto-registration to check its ok to register this user
-
- @param username: the users email address
- @param password: the plain text passord they typed
- @param options: dictionary of options provided by admin in customauth xml config file
- @param debug: boolean, False indicating admin wants debugging information printed
- @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
- '''
-
+ """
+ See abstract method documentation.
+ """
if debug:
print ("Username: %s" % username)
print ("Options: %s" % options)
-
+
failuremode = False # reject but continue
- if _getopt(options, 'continue-on-failure', 'False') == 'False':
+ if options.get('continue-on-failure', 'False') == 'False':
failuremode = None # reject and do not continue
-
+
try:
import ldap
except:
if debug:
print ("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
return (failuremode, '')
-
+
## do AD search (if required) ##
vars = {'username': username, 'password': password}
if 'search-fields' in options:
@@ -65,11 +52,11 @@
l.protocol_version = 3
l.simple_bind_s(_getsubs(options,'search-user',vars), _getsubs(options,'search-password',vars))
scope = ldap.SCOPE_SUBTREE
-
+
# setup search
attributes = map(lambda s: s.strip().format(**vars), options['search-fields'].split(','))
result = l.search(_getsubs(options,'search-base',vars), scope, _getsubs(options,'search-filter',vars), attributes)
-
+
# parse results
_,suser = l.result(result,60)
_,attrs = suser[0]
@@ -86,7 +73,7 @@
print('User: %s, ACTIVEDIRECTORY: Search Exception:\n%s' % (username, traceback.format_exc(),))
return (failuremode, '')
# end search
-
+
# bind as user to check their credentials
try:
# setup connection
@@ -98,22 +85,13 @@
if debug:
print('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc(),))
return (failuremode, '')
-
+
if debug:
print "User: %s, ACTIVEDIRECTORY: True" % (username)
return (True, _getsubs(options,'auto-register-username',vars))
-
+
def authenticateUser(self, user, password, options, debug=False):
- '''
- Same as authenticate, except User object is provided instead of username.
-
- NOTE: used on normal login to check authentication and update user details if required.
-
- @param username: the users email address
- @param password: the plain text passord they typed
- @param options: dictionary of options provided by admin in customauth xml config file
- @param debug: boolean, False indicating admin wants debugging information printed
- @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
- '''
-
+ """
+ See abstract method documentation.
+ """
return self.authenticate(user.email, password, options, debug)[0]
diff -r 8ae0eb0b556790796c2da2477db0fcd777ae13a7 -r 5ae99e2427746abb436eb82231372c69a61017e0 lib/galaxy/customauth/providers/alwaysreject.py
--- a/lib/galaxy/customauth/providers/alwaysreject.py
+++ b/lib/galaxy/customauth/providers/alwaysreject.py
@@ -1,42 +1,26 @@
-'''
+"""
Created on 16/07/2014
@author: Andrew Robinson
-'''
+"""
-import traceback
import galaxy.customauth.base
class AlwaysReject(galaxy.customauth.base.CustomAuthProvider):
- '''A simple authenticator that just accepts user (doesn't care about their password)'''
-
+ """A simple authenticator that just accepts users (does not care about their
+ password).
+ """
+
def authenticate(self, username, password, options, debug=False):
- '''
- Check the username and password are correct.
-
- NOTE: Used within auto-registration to check its ok to register this user
-
- @param username: the users email address
- @param password: the plain text passord they typed
- @param options: dictionary of options provided by admin in customauth xml config file
- @param debug: boolean, False indicating admin wants debugging information printed
- @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
- '''
+ """
+ See abstract method documentation.
+ """
return (None, '')
-
+
def authenticateUser(self, user, password, options, debug=False):
- '''
- Same as authenticate, except User object is provided instead of username.
-
- NOTE: used on normal login to check authentication and update user details if required.
-
- @param username: the users email address
- @param password: the plain text passord they typed
- @param options: dictionary of options provided by admin in customauth xml config file
- @param debug: boolean, False indicating admin wants debugging information printed
- @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
- '''
-
+ """
+ See abstract method documentation.
+ """
if debug:
print ("User: %s, ALWAYSREJECT: None" % (user.email))
return None
diff -r 8ae0eb0b556790796c2da2477db0fcd777ae13a7 -r 5ae99e2427746abb436eb82231372c69a61017e0 lib/galaxy/customauth/providers/localdb.py
--- a/lib/galaxy/customauth/providers/localdb.py
+++ b/lib/galaxy/customauth/providers/localdb.py
@@ -1,43 +1,24 @@
-'''
+"""
Created on 16/07/2014
@author: Andrew Robinson
-'''
+"""
-import traceback
import galaxy.customauth.base
class LocalDB(galaxy.customauth.base.CustomAuthProvider):
- '''Checks against local DB (as per usual)'''
-
+ """Authenticate users against the local Galaxy database (as per usual)."""
+
def authenticate(self, username, password, options, debug=False):
- '''
- Check the username and password are correct.
-
- NOTE: Used within auto-registration to check its ok to register this user
-
- @param username: the users email address
- @param password: the plain text passord they typed
- @param options: dictionary of options provided by admin in customauth xml config file
- @param debug: boolean, False indicating admin wants debugging information printed
- @return: (boolean, str), True: accept user, False: reject user and None: reject user and don't try any other providers. str is the username to register with if accepting.
- '''
-
+ """
+ See abstract method documentation.
+ """
return (False, '') # it can never auto-create based of localdb (chicken-egg)
-
+
def authenticateUser(self, user, password, options, debug=False):
- '''
- Same as authenticate, except User object is provided instead of username.
-
- NOTE: used on normal login to check authentication and update user details if required.
-
- @param username: the users email address
- @param password: the plain text passord they typed
- @param options: dictionary of options provided by admin in customauth xml config file
- @param debug: boolean, False indicating admin wants debugging information printed
- @return: boolean, True: accept user, False: reject user and None: reject user and don't try any other providers
- '''
-
+ """
+ See abstract method documentation.
+ """
user_ok = user.check_password(password)
if debug:
print ("User: %s, LOCALDB: %s" % (user.email, user_ok))
diff -r 8ae0eb0b556790796c2da2477db0fcd777ae13a7 -r 5ae99e2427746abb436eb82231372c69a61017e0 lib/galaxy/webapps/galaxy/api/authenticate.py
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -46,18 +46,18 @@
user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).all()
- if ( len( user ) == 0 ):
+ if len( user ) == 0:
raise exceptions.ObjectNotFound( 'The user does not exist.' )
- elif ( len( user ) > 1 ):
+ elif len( user ) > 1:
# DB is inconsistent and we have more users with the same email.
raise exceptions.InconsistentDatabase( 'An error occured, please contact your administrator.' )
else:
user = user[0]
- if (trans.app.config.enable_customauth):
+ if trans.app.config.enable_customauth:
is_valid_user = galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
else:
is_valid_user = user.check_password( password )
- if ( is_valid_user ):
+ if is_valid_user:
key = self.api_keys_manager.get_or_create_api_key( user )
return dict( api_key=key )
else:
diff -r 8ae0eb0b556790796c2da2477db0fcd777ae13a7 -r 5ae99e2427746abb436eb82231372c69a61017e0 lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -681,7 +681,7 @@
# check user is allowed to register
message = ''
if trans.app.config.enable_customauth:
- message, status = galaxy.customauth.check_registration_allowed(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
+ message, status = galaxy.customauth.check_registration_allowed(email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
if message == '':
if not refresh_frames:
if trans.webapp.name == 'galaxy':
https://bitbucket.org/galaxy/galaxy-central/commits/868d69d100d2/
Changeset: 868d69d100d2
User: nsoranzo
Date: 2015-02-17 21:44:28+00:00
Summary: Make customauth always active.
Added a config/customauth_conf.xml.sample file containing only the normal
Galaxy database authentication method.
Removed enable_customauth config option.
Affected #: 6 files
diff -r 5ae99e2427746abb436eb82231372c69a61017e0 -r 868d69d100d2aa855df35efb91ba418fef6491dd config/customauth_conf.xml.sample
--- /dev/null
+++ b/config/customauth_conf.xml.sample
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<customauth>
+ <authenticator>
+ <type>localdb</type>
+ </authenticator>
+</customauth>
diff -r 5ae99e2427746abb436eb82231372c69a61017e0 -r 868d69d100d2aa855df35efb91ba418fef6491dd config/galaxy.ini.sample
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -844,9 +844,9 @@
#openid_config_file = config/openid_conf.xml
#openid_consumer_cache_path = database/openid_consumer_cache
-# Enable the use of custom authentication providers. Allows users to use their
-# Active Directory (or other) account instead of local authentication.
-#enable_customauth = False
+# XML config file that allows the use of custom authentication providers (e.g.
+# Active Directory) instead or in addition to local authentication (.sample is
+# used if default does not exist).
#customauth_config_file = config/customauth_conf.xml
# Print debugging info for customauth
#customauth_debug = False
diff -r 5ae99e2427746abb436eb82231372c69a61017e0 -r 868d69d100d2aa855df35efb91ba418fef6491dd lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -442,8 +442,6 @@
# Default chunk size for chunkable datatypes -- 64k
self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) )
# customauth
- self.enable_customauth = string_as_bool( kwargs.get( 'enable_customauth', False ) )
- self.customauth_config_file = resolve_path( kwargs.get( 'customauth_config_file', 'config/customauth_conf.xml' ), self.root )
self.customauth_debug = string_as_bool( kwargs.get( 'customauth_debug', False ) )
self.citation_cache_type = kwargs.get( "citation_cache_type", "file" )
@@ -466,6 +464,7 @@
Backwards compatibility for config files moved to the config/ dir.
"""
defaults = dict(
+ customauth_config_file=[ 'config/customauth_conf.xml', 'config/customauth_conf.xml.sample' ],
data_manager_config_file=[ 'config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample' ],
datatypes_config_file=[ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ],
external_service_type_config_file=[ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ],
diff -r 5ae99e2427746abb436eb82231372c69a61017e0 -r 868d69d100d2aa855df35efb91ba418fef6491dd lib/galaxy/webapps/galaxy/api/authenticate.py
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -53,10 +53,7 @@
raise exceptions.InconsistentDatabase( 'An error occured, please contact your administrator.' )
else:
user = user[0]
- if trans.app.config.enable_customauth:
- is_valid_user = galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
- else:
- is_valid_user = user.check_password( password )
+ is_valid_user = galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
if is_valid_user:
key = self.api_keys_manager.get_or_create_api_key( user )
return dict( api_key=key )
diff -r 5ae99e2427746abb436eb82231372c69a61017e0 -r 868d69d100d2aa855df35efb91ba418fef6491dd lib/galaxy/webapps/galaxy/controllers/mobile.py
--- a/lib/galaxy/webapps/galaxy/controllers/mobile.py
+++ b/lib/galaxy/webapps/galaxy/controllers/mobile.py
@@ -59,35 +59,31 @@
# error = password_error = None
# user = trans.sa_session.query( model.User ).filter_by( email = email ).first()
# if not user:
- # if trans.app.config.enable_customauth:
- # autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
- # if autoreg[0]:
- # kwd = {}
- # kwd['username'] = autoreg[1]
- # params = util.Params( kwd )
- # message = validate_email( trans, email )
- # if not message:
- # message, status, user, success = self.__register( trans, 'user', False, **kwd )
- # if success:
- # The handle_user_login() method has a call to the history_set_default_permissions() method
- # (needed when logging in with a history), user needs to have default permissions set before logging in
- # trans.handle_user_login( user )
- # trans.log_event( "User (auto) created a new account" )
- # trans.log_event( "User logged in" )
- # else:
- # message = "Auto-registration failed, contact your local Galaxy administrator. %s" %message
+ # autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
+ # if autoreg[0]:
+ # kwd = {}
+ # kwd['username'] = autoreg[1]
+ # params = util.Params( kwd )
+ # message = validate_email( trans, email )
+ # if not message:
+ # message, status, user, success = self.__register( trans, 'user', False, **kwd )
+ # if success:
+ # # The handle_user_login() method has a call to the history_set_default_permissions() method
+ # # (needed when logging in with a history), user needs to have default permissions set before logging in
+ # trans.handle_user_login( user )
+ # trans.log_event( "User (auto) created a new account" )
+ # trans.log_event( "User logged in" )
# else:
- # message = "Auto-registration failed, contact your local Galaxy administrator. %s" %message
+ # message = "Auto-registration failed, contact your local Galaxy administrator. %s" % message
# else:
- # message = "No such user (please note that login is case sensitive)"
+ # message = "Auto-registration failed, contact your local Galaxy administrator. %s" % message
# else:
# message = "No such user (please note that login is case sensitive)"
# elif user.deleted:
# error = "This account has been marked deleted, contact your Galaxy administrator to restore the account."
# elif user.external:
# error = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it."
- # elif not trans.app.config.enable_customauth and not user.check_password( password ) or \
- # trans.app.config.enable_customauth and not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug):
+ # elif not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug):
# error = "Invalid password"
# else:
# trans.handle_user_login( user )
diff -r 5ae99e2427746abb436eb82231372c69a61017e0 -r 868d69d100d2aa855df35efb91ba418fef6491dd lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -515,32 +515,28 @@
success = False
user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first()
if trans.app.config.customauth_debug:
- print ("trans.app.config.enable_customauth: %s" % trans.app.config.enable_customauth)
print ("trans.app.config.customauth_config_file: %s" % trans.app.config.customauth_config_file)
print ("trans.app.config.customauth_debug: %s WARNING: don't use in production" % trans.app.config.customauth_debug)
if not user:
- if trans.app.config.enable_customauth:
- autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
- if autoreg[0]:
- kwd['username'] = autoreg[1]
- params = util.Params( kwd )
- message = validate_email( trans, email ) #self.__validate( trans, params, email, password, password, username )
- if not message:
- message, status, user, success = self.__register( trans, 'user', False, **kwd )
- if success:
- # The handle_user_login() method has a call to the history_set_default_permissions() method
- # (needed when logging in with a history), user needs to have default permissions set before logging in
- trans.handle_user_login( user )
- trans.log_event( "User (auto) created a new account" )
- trans.log_event( "User logged in" )
- else:
- message = "Auto-registration failed, contact your local Galaxy administrator. %s" %message
+ autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
+ if autoreg[0]:
+ kwd['username'] = autoreg[1]
+ params = util.Params( kwd )
+ message = validate_email( trans, email ) #self.__validate( trans, params, email, password, password, username )
+ if not message:
+ message, status, user, success = self.__register( trans, 'user', False, **kwd )
+ if success:
+ # The handle_user_login() method has a call to the history_set_default_permissions() method
+ # (needed when logging in with a history), user needs to have default permissions set before logging in
+ trans.handle_user_login( user )
+ trans.log_event( "User (auto) created a new account" )
+ trans.log_event( "User logged in" )
else:
- message = "Auto-registration failed, contact your local Galaxy administrator. %s" %message
+ message = "Auto-registration failed, contact your local Galaxy administrator. %s" % message
else:
- message = "No such user or invalid password"
+ message = "Auto-registration failed, contact your local Galaxy administrator. %s" % message
else:
- message = "No such user (please note that login is case sensitive)"
+ message = "No such user or invalid password"
elif user.deleted:
message = "This account has been marked deleted, contact your local Galaxy administrator to restore the account."
if trans.app.config.error_email_to is not None:
@@ -549,8 +545,7 @@
message = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it."
if trans.app.config.error_email_to is not None:
message += ' Contact: %s' % trans.app.config.error_email_to
- elif not trans.app.config.enable_customauth and not user.check_password( password ) or \
- trans.app.config.enable_customauth and not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug):
+ elif not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug):
message = "Invalid password"
elif trans.app.config.user_activation_on and not user.active: # activation is ON and the user is INACTIVE
if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON
@@ -679,9 +674,7 @@
status = 'error'
else:
# check user is allowed to register
- message = ''
- if trans.app.config.enable_customauth:
- message, status = galaxy.customauth.check_registration_allowed(email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
+ message, status = galaxy.customauth.check_registration_allowed(email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
if message == '':
if not refresh_frames:
if trans.webapp.name == 'galaxy':
@@ -1132,16 +1125,10 @@
return trans.show_error_message("Invalid or expired password reset token, please request a new one.")
else:
# The user is changing their own password, validate their current password
- if trans.app.config.enable_customauth:
- (ok, message) = galaxy.customauth.check_change_password(trans.user, current, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
- if ok:
- user = trans.user
- else:
- status = "error"
- elif trans.user.check_password( current ):
+ (ok, message) = galaxy.customauth.check_change_password(trans.user, current, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
+ if ok:
user = trans.user
else:
- message = 'Invalid current password'
status = 'error'
if user:
# Validate the new password
https://bitbucket.org/galaxy/galaxy-central/commits/8d0ea77d02b4/
Changeset: 8d0ea77d02b4
User: nsoranzo
Date: 2015-02-20 18:20:40+00:00
Summary: Rename CustomAuth to Auth.
Affected #: 25 files
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 config/auth_conf.xml.sample
--- /dev/null
+++ b/config/auth_conf.xml.sample
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<auth>
+ <authenticator>
+ <type>localdb</type>
+ </authenticator>
+</auth>
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 config/customauth_conf.xml.sample
--- a/config/customauth_conf.xml.sample
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<customauth>
- <authenticator>
- <type>localdb</type>
- </authenticator>
-</customauth>
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 config/galaxy.ini.sample
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -844,12 +844,12 @@
#openid_config_file = config/openid_conf.xml
#openid_consumer_cache_path = database/openid_consumer_cache
-# XML config file that allows the use of custom authentication providers (e.g.
-# Active Directory) instead or in addition to local authentication (.sample is
-# used if default does not exist).
-#customauth_config_file = config/customauth_conf.xml
-# Print debugging info for customauth
-#customauth_debug = False
+# XML config file that allows the use of different authentication providers
+# (e.g. Active Directory) instead or in addition to local authentication
+# (.sample is used if default does not exist).
+#auth_config_file = config/auth_conf.xml
+# Print debugging info for auth
+#auth_debug = False
# Optional list of email addresses of API users who can make calls on behalf of
# other users.
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/auth/__init__.py
--- /dev/null
+++ b/lib/galaxy/auth/__init__.py
@@ -0,0 +1,192 @@
+"""
+Contains implementations of the authentication logic.
+"""
+
+import traceback
+import xml.etree.ElementTree
+from yapsy.PluginManager import PluginManager
+
+from galaxy.security.validate_user_input import validate_publicname
+
+import logging
+logging.basicConfig(level=logging.DEBUG)
+
+# <auth>
+# <authenticator>
+# <type>activedirectory</type>
+# <filter>'[username]'.endswith('@students.latrobe.edu.au')</filter>
+# <options>
+# <auto-register>True</auto-register>
+# <server>ldap://STUDENTS.ltu.edu.au</server>
+# [<search-filter>(&(objectClass=user)(mail={username}))</search-filter>
+# <search-base>dc=STUDENTS,dc=ltu,dc=edu,dc=au</search-base>
+# <search-user>jsmith</search-user>
+# <search-password>mysecret</search-password>
+# <search-fields>sAMAccountName</search-fields>]
+# <bind-user>{sAMAccountName}(a)STUDENTS.ltu.edu.au</bind-user>
+# <bind-password>{password}</bind-password>
+# <auto-register-username>{sAMAccountName}</auto-register-username>
+# </options>
+# </authenticator>
+# ...
+# </auth>
+
+def check_registration_allowed(email, password, configfile, debug=False):
+ """Checks if the provided email is allowed to register."""
+ message = ''
+ status = 'done'
+ for provider, options in activeAuthProviderGenerator(email, password, configfile, debug):
+ allowreg = _getTriState(options, 'allow-register', True)
+ if allowreg is None: # i.e. challenge
+ authresult, msg = provider.authenticate(email, password, options, debug)
+ if authresult == True:
+ break
+ if authresult is None:
+ message = 'Invalid email address or password'
+ status = 'error'
+ break
+ elif allowreg is True:
+ break
+ elif allowreg is False:
+ message = 'Account registration not required for your account. Please simply login.'
+ status = 'error'
+ break
+ return message, status
+
+def check_auto_registration(trans, email, password, configfile, debug=False):
+ """
+ Checks the email/password using auth providers in order. If a match is
+ found, returns the 'auto-register' option for that provider.
+ """
+ for provider, options in activeAuthProviderGenerator(email, password, configfile, debug):
+ if provider is None:
+ if debug:
+ print "Unable to find module: %s" % options
+ else:
+ authresult, autousername = provider.authenticate(email, password, options, debug)
+ autousername = str(autousername).lower()
+ if authresult is True:
+ # make username unique
+ if validate_publicname( trans, autousername ) != '':
+ i = 1
+ while i <= 10: # stop after 10 tries
+ if validate_publicname( trans, "%s-%i" % (autousername, i) ) == '':
+ autousername = "%s-%i" % (autousername, i)
+ break
+ i += 1
+ else:
+ break # end for loop if we can't make a unique username
+ if debug:
+ print "Email: %s, auto-register with username: %s" % (email, autousername)
+ return (_getBool(options, 'auto-register', False), autousername)
+ elif authresult is None:
+ print "Email: %s, stopping due to failed non-continue" % (email)
+ break # end authentication (skip rest)
+ return (False, '')
+
+def check_password(user, password, configfile, debug=False):
+ """Checks the email/password using auth providers."""
+ for provider, options in activeAuthProviderGenerator(user.email, password, configfile, debug):
+ if provider is None:
+ if debug:
+ print "Unable to find module: %s" % options
+ else:
+ authresult = provider.authenticateUser(user, password, options, debug)
+ if authresult is True:
+ return True # accept user
+ elif authresult is None:
+ break # end authentication (skip rest)
+ return False
+
+def check_change_password(user, current_password, configfile, debug=False):
+ """Checks that auth provider allows password changes and current_password
+ matches.
+ """
+ for provider, options in activeAuthProviderGenerator(user.email, current_password, configfile, debug):
+ if provider is None:
+ if debug:
+ print "Unable to find module: %s" % options
+ else:
+ if _getBool(options, "allow-password-change", False):
+ authresult = provider.authenticateUser(user, current_password, options, debug)
+ if authresult is True:
+ return (True, '') # accept user
+ elif authresult is None:
+ break # end authentication (skip rest)
+ else:
+ return (False, 'Password change not supported')
+ return (False, 'Invalid current password')
+
+def activeAuthProviderGenerator(username, password, configfile, debug):
+ """Yields AuthProvider instances for the provided configfile that match the
+ filters.
+ """
+ try:
+ # load the yapsy plugins
+ manager = PluginManager()
+ manager.setPluginPlaces(["lib/galaxy/auth/providers"])
+ manager.collectPlugins()
+
+ if debug:
+ print ("Plugins found:")
+ for plugin in manager.getAllPlugins():
+ print ("- %s" % (plugin.path))
+
+ # parse XML
+ ct = xml.etree.ElementTree.parse(configfile)
+ confroot = ct.getroot()
+
+ # process authenticators
+ for authelem in confroot.getchildren():
+ typeelem = authelem.iter('type').next()
+
+ # check filterelem
+ filterelem = _getChildElement(authelem, 'filter')
+ if filterelem is not None:
+ filterstr = str(filterelem.text).format(username=username, password=password)
+ if debug:
+ print ("Filter: %s == %s" % (filterstr, eval(filterstr, {"__builtins__":None},{'str':str})))
+ if not eval(filterstr, {"__builtins__":None},{'str':str}):
+ continue # skip to next
+
+ # extract options
+ optionselem = _getChildElement(authelem, 'options')
+ options = {}
+ if optionselem is not None:
+ for opt in optionselem:
+ options[opt.tag] = opt.text
+
+ # get the instance
+ plugin = manager.getPluginByName(typeelem.text)
+ yield (plugin.plugin_object, options) # excepts if type is spelled incorrectly
+ except GeneratorExit:
+ return
+ except:
+ if debug:
+ print ('Auth: Exception:\n%s' % (traceback.format_exc(),))
+
+def _getBool(d, k, o):
+ if k in d:
+ if d[k] in ('True', 'true', 'Yes', 'yes', '1', 1, True):
+ return True
+ else:
+ return False
+ else:
+ return o
+
+def _getTriState(d, k, o):
+ if k in d:
+ if d[k] in ('True', 'true', 'Yes', 'yes', '1', 1, True):
+ return True
+ elif d[k] in ('False', 'false', 'No', 'no', '0', 0, False):
+ return False
+ else:
+ return None
+ else:
+ return o
+
+def _getChildElement(parent, childname):
+ try:
+ return parent.iter(childname).next()
+ except StopIteration:
+ return None
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/auth/base.py
--- /dev/null
+++ b/lib/galaxy/auth/base.py
@@ -0,0 +1,54 @@
+"""
+Created on 15/07/2014
+
+@author: Andrew Robinson
+"""
+
+from yapsy.IPlugin import IPlugin
+
+class AuthProvider(IPlugin):
+ """A base class for all Auth Providers."""
+
+ def authenticate(self, username, password, options, debug=False):
+ """
+ Check that the username and password are correct.
+
+ NOTE: Used within auto-registration to check it is ok to register this
+ user.
+
+ :param username: the users email address
+ :type username: str
+ :param password: the plain text password they typed
+ :type password: str
+ :param options: options provided in auth_config_file
+ :type options: dict
+ :param debug: whether to print debugging info (defaults to False)
+ :type debug: bool
+ :returns: True: accept user, False: reject user and None: reject user
+ and don't try any other providers. str is the username to register
+ with if accepting
+ :rtype: (bool, str)
+ """
+ raise NotImplementedError()
+
+ def authenticateUser(self, user, password, options, debug=False):
+ """
+ Same as authenticate() method, except an User object is provided instead
+ of a username.
+
+ NOTE: used on normal login to check authentication and update user
+ details if required.
+
+ :param username: the users email address
+ :type username: str
+ :param password: the plain text password they typed
+ :type password: str
+ :param options: options provided in auth_config_file
+ :type options: dict
+ :param debug: whether to print debugging info (defaults to False)
+ :type debug: bool
+ :returns: True: accept user, False: reject user and None: reject user
+ and don't try any other providers
+ :rtype: bool
+ """
+ raise NotImplementedError()
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/auth/providers/activedirectory.py
--- /dev/null
+++ b/lib/galaxy/auth/providers/activedirectory.py
@@ -0,0 +1,97 @@
+"""
+Created on 15/07/2014
+
+@author: Andrew Robinson
+"""
+
+import traceback
+import galaxy.auth.base
+
+
+def _getsubs(d, k, vars, default=''):
+ if k in d:
+ return str(d[k]).format(**vars)
+ return str(default).format(**vars)
+
+
+class ActiveDirectory(galaxy.auth.base.AuthProvider):
+ """
+ Attempts to authenticate users against an Active Directory server.
+
+ If options include search-fields then it will attempt to search the AD for
+ those fields first. After that it will bind to the AD with the username
+ (formatted as specified).
+ """
+
+ def authenticate(self, username, password, options, debug=False):
+ """
+ See abstract method documentation.
+ """
+ if debug:
+ print ("Username: %s" % username)
+ print ("Options: %s" % options)
+
+ failuremode = False # reject but continue
+ if options.get('continue-on-failure', 'False') == 'False':
+ failuremode = None # reject and do not continue
+
+ try:
+ import ldap
+ except:
+ if debug:
+ print ("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
+ return (failuremode, '')
+
+ ## do AD search (if required) ##
+ vars = {'username': username, 'password': password}
+ if 'search-fields' in options:
+ try:
+ # setup connection
+ ldap.set_option(ldap.OPT_REFERRALS, 0)
+ l = ldap.initialize(_getsubs(options,'server',vars))
+ l.protocol_version = 3
+ l.simple_bind_s(_getsubs(options,'search-user',vars), _getsubs(options,'search-password',vars))
+ scope = ldap.SCOPE_SUBTREE
+
+ # setup search
+ attributes = map(lambda s: s.strip().format(**vars), options['search-fields'].split(','))
+ result = l.search(_getsubs(options,'search-base',vars), scope, _getsubs(options,'search-filter',vars), attributes)
+
+ # parse results
+ _,suser = l.result(result,60)
+ _,attrs = suser[0]
+ if debug:
+ print ("AD Search attributes: %s" % attrs)
+ if hasattr(attrs, 'has_key'):
+ for attr in attributes:
+ if attrs.has_key(attr):
+ vars[attr] = str(attrs[attr][0])
+ else:
+ vars[attr] = ""
+ except Exception:
+ if debug:
+ print('User: %s, ACTIVEDIRECTORY: Search Exception:\n%s' % (username, traceback.format_exc(),))
+ return (failuremode, '')
+ # end search
+
+ # bind as user to check their credentials
+ try:
+ # setup connection
+ ldap.set_option(ldap.OPT_REFERRALS, 0)
+ l = ldap.initialize(_getsubs(options,'server',vars))
+ l.protocol_version = 3
+ l.simple_bind_s(_getsubs(options,'bind-user',vars), _getsubs(options,'bind-password',vars))
+ except Exception:
+ if debug:
+ print('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc(),))
+ return (failuremode, '')
+
+ if debug:
+ print "User: %s, ACTIVEDIRECTORY: True" % (username)
+ return (True, _getsubs(options,'auto-register-username',vars))
+
+ def authenticateUser(self, user, password, options, debug=False):
+ """
+ See abstract method documentation.
+ """
+ return self.authenticate(user.email, password, options, debug)[0]
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/auth/providers/activedirectory.yapsy-plugin
--- /dev/null
+++ b/lib/galaxy/auth/providers/activedirectory.yapsy-plugin
@@ -0,0 +1,8 @@
+[Core]
+Name = ActiveDirectory
+Module = activedirectory
+
+[Documentation]
+Author = Andrew Robinson
+Version = 0.1
+Description = Authentication Provider that authenticates against an ActiveDirectory (via LDAP). Requires python-ldap module.
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/auth/providers/alwaysreject.py
--- /dev/null
+++ b/lib/galaxy/auth/providers/alwaysreject.py
@@ -0,0 +1,26 @@
+"""
+Created on 16/07/2014
+
+@author: Andrew Robinson
+"""
+
+import galaxy.auth.base
+
+class AlwaysReject(galaxy.auth.base.AuthProvider):
+ """A simple authenticator that just accepts users (does not care about their
+ password).
+ """
+
+ def authenticate(self, username, password, options, debug=False):
+ """
+ See abstract method documentation.
+ """
+ return (None, '')
+
+ def authenticateUser(self, user, password, options, debug=False):
+ """
+ See abstract method documentation.
+ """
+ if debug:
+ print ("User: %s, ALWAYSREJECT: None" % (user.email))
+ return None
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/auth/providers/alwaysreject.yapsy-plugin
--- /dev/null
+++ b/lib/galaxy/auth/providers/alwaysreject.yapsy-plugin
@@ -0,0 +1,8 @@
+[Core]
+Name = AlwaysReject
+Module = alwaysreject
+
+[Documentation]
+Author = Andrew Robinson
+Version = 0.1
+Description = Authentication Provider that is used for blacklisting usernames (i.e. accept no password)
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/auth/providers/localdb.py
--- /dev/null
+++ b/lib/galaxy/auth/providers/localdb.py
@@ -0,0 +1,25 @@
+"""
+Created on 16/07/2014
+
+@author: Andrew Robinson
+"""
+
+import galaxy.auth.base
+
+class LocalDB(galaxy.auth.base.AuthProvider):
+ """Authenticate users against the local Galaxy database (as per usual)."""
+
+ def authenticate(self, username, password, options, debug=False):
+ """
+ See abstract method documentation.
+ """
+ return (False, '') # it can never auto-create based of localdb (chicken-egg)
+
+ def authenticateUser(self, user, password, options, debug=False):
+ """
+ See abstract method documentation.
+ """
+ user_ok = user.check_password(password)
+ if debug:
+ print ("User: %s, LOCALDB: %s" % (user.email, user_ok))
+ return user_ok
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/auth/providers/localdb.yapsy-plugin
--- /dev/null
+++ b/lib/galaxy/auth/providers/localdb.yapsy-plugin
@@ -0,0 +1,8 @@
+[Core]
+Name = LocalDB
+Module = localdb
+
+[Documentation]
+Author = Andrew Robinson
+Version = 0.1
+Description = Authentication Provider that checks against the local database as per normal.
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -441,8 +441,8 @@
# Default chunk size for chunkable datatypes -- 64k
self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) )
- # customauth
- self.customauth_debug = string_as_bool( kwargs.get( 'customauth_debug', False ) )
+ # auth
+ self.auth_debug = string_as_bool( kwargs.get( 'auth_debug', False ) )
self.citation_cache_type = kwargs.get( "citation_cache_type", "file" )
self.citation_cache_data_dir = self.resolve_path( kwargs.get( "citation_cache_data_dir", "database/citations/data" ) )
@@ -464,7 +464,7 @@
Backwards compatibility for config files moved to the config/ dir.
"""
defaults = dict(
- customauth_config_file=[ 'config/customauth_conf.xml', 'config/customauth_conf.xml.sample' ],
+ auth_config_file=[ 'config/auth_conf.xml', 'config/auth_conf.xml.sample' ],
data_manager_config_file=[ 'config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample' ],
datatypes_config_file=[ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ],
external_service_type_config_file=[ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ],
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/customauth/__init__.py
--- a/lib/galaxy/customauth/__init__.py
+++ /dev/null
@@ -1,196 +0,0 @@
-"""
-Contains implementations of custom auth logic.
-"""
-
-import traceback
-import xml.etree.ElementTree
-from yapsy.PluginManager import PluginManager
-
-from galaxy.security.validate_user_input import validate_publicname
-
-import logging
-logging.basicConfig(level=logging.DEBUG)
-
-# <customauth>
-# <authenticator>
-# <type>activedirectory</type>
-# <filter>'[username]'.endswith('@students.latrobe.edu.au')</filter>
-# <options>
-# <auto-register>True</auto-register>
-# <server>ldap://STUDENTS.ltu.edu.au</server>
-# [<search-filter>(&(objectClass=user)(mail={username}))</search-filter>
-# <search-base>dc=STUDENTS,dc=ltu,dc=edu,dc=au</search-base>
-# <search-user>jsmith</search-user>
-# <search-password>mysecret</search-password>
-# <search-fields>sAMAccountName</search-fields>]
-# <bind-user>{sAMAccountName}(a)STUDENTS.ltu.edu.au</bind-user>
-# <bind-password>{password}</bind-password>
-# <auto-register-username>{sAMAccountName}</auto-register-username>
-# </options>
-# </authenticator>
-# ...
-# </customauth>
-
-def check_registration_allowed(email, password, configfile, debug=False):
- """Checks if the provided email is allowed to register."""
- message = ''
- status = 'done'
- for provider, options in activeAuthProviderGenerator(email, password, configfile, debug):
- allowreg = _getTriState(options, 'allow-register', True)
- if allowreg is None: # i.e. challenge
- authresult, msg = provider.authenticate(email, password, options, debug)
- if authresult == True:
- break
- if authresult is None:
- message = 'Invalid email address or password'
- status = 'error'
- break
- elif allowreg is True:
- break
- elif allowreg is False:
- message = 'Account registration not required for your account. Please simply login.'
- status = 'error'
- break
- return message, status
-
-def check_auto_registration(trans, email, password, configfile, debug=False):
- """Checks the email/password using custom auth providers and if matches
- returns the 'auto-register' option for that provider.
- """
- for provider, options in activeAuthProviderGenerator(email, password, configfile, debug):
- if provider is None:
- if debug:
- print "Unable to find module: %s" % options
- else:
- authresult, autousername = provider.authenticate(email, password, options, debug)
- autousername = str(autousername).lower()
- if authresult is True:
- # make username unique
- if validate_publicname( trans, autousername ) != '':
- i = 1
- while i <= 10: # stop after 10 tries
- if validate_publicname( trans, "%s-%i" % (autousername, i) ) == '':
- autousername = "%s-%i" % (autousername, i)
- break
- i += 1
- else:
- break # end for loop if we can't make a unique username
- if debug:
- print "Email: %s, auto-register with username: %s" % (email, autousername)
- return (_getBool(options, 'auto-register', False), autousername)
- elif authresult is None:
- print "Email: %s, stopping due to failed non-continue" % (email)
- break # end authentication (skip rest)
- return (False, '')
-
-def check_password(user, password, configfile, debug=False):
- """Checks the email/password using custom auth providers."""
- if debug:
- print ("Checking with CustomAuth")
-
- for provider, options in activeAuthProviderGenerator(user.email, password, configfile, debug):
- if provider is None:
- if debug:
- print "Unable to find module: %s" % options
- else:
- authresult = provider.authenticateUser(user, password, options, debug)
- if authresult is True:
- return True # accept user
- elif authresult is None:
- break # end authentication (skip rest)
- return False
-
-def check_change_password(user, current_password, configfile, debug=False):
- """Checks that provider allows password changes and current_password
- matches.
- """
- if debug:
- print ("Checking password change with CustomAuth")
- for provider, options in activeAuthProviderGenerator(user.email, current_password, configfile, debug):
- if provider is None:
- if debug:
- print "Unable to find module: %s" % options
- else:
- if _getBool(options, "allow-password-change", False):
- authresult = provider.authenticateUser(user, current_password, options, debug)
- if authresult is True:
- return (True, '') # accept user
- elif authresult is None:
- break # end authentication (skip rest)
- else:
- return (False, 'Password change not supported')
- return (False, 'Invalid current password')
-
-def activeAuthProviderGenerator(username, password, configfile, debug):
- """Yields CustomAuthProvider instances for the provided configfile that
- match the filters.
- """
- try:
- # load the yapsy plugins
- manager = PluginManager()
- manager.setPluginPlaces(["lib/galaxy/customauth/providers"])
- manager.collectPlugins()
-
- if debug:
- print ("Plugins found:")
- for plugin in manager.getAllPlugins():
- print ("- %s" % (plugin.path))
-
- # parse XML
- ct = xml.etree.ElementTree.parse(configfile)
- confroot = ct.getroot()
-
- # process authenticators
- for authelem in confroot.getchildren():
- typeelem = authelem.iter('type').next()
-
- # check filterelem
- filterelem = _getChildElement(authelem, 'filter')
- if filterelem is not None:
- filterstr = str(filterelem.text).format(username=username, password=password)
- if debug:
- print ("Filter: %s == %s" % (filterstr, eval(filterstr, {"__builtins__":None},{'str':str})))
- if not eval(filterstr, {"__builtins__":None},{'str':str}):
- continue # skip to next
-
- # extract options
- optionselem = _getChildElement(authelem, 'options')
- options = {}
- if optionselem is not None:
- for opt in optionselem:
- options[opt.tag] = opt.text
-
- # get the instance
- plugin = manager.getPluginByName(typeelem.text)
- yield (plugin.plugin_object, options) # excepts if type is spelled incorrectly
- except GeneratorExit:
- return
- except:
- if debug:
- print ('CustomAuth: Exception:\n%s' % (traceback.format_exc(),))
-
-def _getBool(d, k, o):
- if k in d:
- if d[k] in ('True', 'true', 'Yes', 'yes', '1', 1, True):
- return True
- else:
- return False
- else:
- return o
-
-def _getTriState(d, k, o):
- if k in d:
- if d[k] in ('True', 'true', 'Yes', 'yes', '1', 1, True):
- return True
- elif d[k] in ('False', 'false', 'No', 'no', '0', 0, False):
- return False
- else:
- return None
- else:
- return o
-
-def _getChildElement(parent, childname):
- try:
- return parent.iter(childname).next()
- except StopIteration:
- return None
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/customauth/base.py
--- a/lib/galaxy/customauth/base.py
+++ /dev/null
@@ -1,54 +0,0 @@
-"""
-Created on 15/07/2014
-
-@author: Andrew Robinson
-"""
-
-from yapsy.IPlugin import IPlugin
-
-class CustomAuthProvider(IPlugin):
- """A base class for all Custom Auth Providers."""
-
- def authenticate(self, username, password, options, debug=False):
- """
- Check that the username and password are correct.
-
- NOTE: Used within auto-registration to check it is ok to register this
- user.
-
- :param username: the users email address
- :type username: str
- :param password: the plain text password they typed
- :type password: str
- :param options: options provided in customauth XML config file
- :type options: dict
- :param debug: whether to print debugging info (defaults to False)
- :type debug: bool
- :returns: True: accept user, False: reject user and None: reject user
- and don't try any other providers. str is the username to register
- with if accepting
- :rtype: (bool, str)
- """
- raise NotImplementedError()
-
- def authenticateUser(self, user, password, options, debug=False):
- """
- Same as authenticate() method, except an User object is provided instead
- of a username.
-
- NOTE: used on normal login to check authentication and update user
- details if required.
-
- :param username: the users email address
- :type username: str
- :param password: the plain text password they typed
- :type password: str
- :param options: options provided in customauth XML config file
- :type options: dict
- :param debug: whether to print debugging info (defaults to False)
- :type debug: bool
- :returns: True: accept user, False: reject user and None: reject user
- and don't try any other providers
- :rtype: bool
- """
- raise NotImplementedError()
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/customauth/providers/activedirectory.py
--- a/lib/galaxy/customauth/providers/activedirectory.py
+++ /dev/null
@@ -1,97 +0,0 @@
-"""
-Created on 15/07/2014
-
-@author: Andrew Robinson
-"""
-
-import traceback
-import galaxy.customauth.base
-
-
-def _getsubs(d, k, vars, default=''):
- if k in d:
- return str(d[k]).format(**vars)
- return str(default).format(**vars)
-
-
-class ActiveDirectory(galaxy.customauth.base.CustomAuthProvider):
- """
- Attempts to authenticate users against an Active Directory server.
-
- If options include search-fields then it will attempt to search the AD for
- those fields first. After that it will bind to the AD with the username
- (formatted as specified).
- """
-
- def authenticate(self, username, password, options, debug=False):
- """
- See abstract method documentation.
- """
- if debug:
- print ("Username: %s" % username)
- print ("Options: %s" % options)
-
- failuremode = False # reject but continue
- if options.get('continue-on-failure', 'False') == 'False':
- failuremode = None # reject and do not continue
-
- try:
- import ldap
- except:
- if debug:
- print ("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
- return (failuremode, '')
-
- ## do AD search (if required) ##
- vars = {'username': username, 'password': password}
- if 'search-fields' in options:
- try:
- # setup connection
- ldap.set_option(ldap.OPT_REFERRALS, 0)
- l = ldap.initialize(_getsubs(options,'server',vars))
- l.protocol_version = 3
- l.simple_bind_s(_getsubs(options,'search-user',vars), _getsubs(options,'search-password',vars))
- scope = ldap.SCOPE_SUBTREE
-
- # setup search
- attributes = map(lambda s: s.strip().format(**vars), options['search-fields'].split(','))
- result = l.search(_getsubs(options,'search-base',vars), scope, _getsubs(options,'search-filter',vars), attributes)
-
- # parse results
- _,suser = l.result(result,60)
- _,attrs = suser[0]
- if debug:
- print ("AD Search attributes: %s" % attrs)
- if hasattr(attrs, 'has_key'):
- for attr in attributes:
- if attrs.has_key(attr):
- vars[attr] = str(attrs[attr][0])
- else:
- vars[attr] = ""
- except Exception:
- if debug:
- print('User: %s, ACTIVEDIRECTORY: Search Exception:\n%s' % (username, traceback.format_exc(),))
- return (failuremode, '')
- # end search
-
- # bind as user to check their credentials
- try:
- # setup connection
- ldap.set_option(ldap.OPT_REFERRALS, 0)
- l = ldap.initialize(_getsubs(options,'server',vars))
- l.protocol_version = 3
- l.simple_bind_s(_getsubs(options,'bind-user',vars), _getsubs(options,'bind-password',vars))
- except Exception:
- if debug:
- print('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc(),))
- return (failuremode, '')
-
- if debug:
- print "User: %s, ACTIVEDIRECTORY: True" % (username)
- return (True, _getsubs(options,'auto-register-username',vars))
-
- def authenticateUser(self, user, password, options, debug=False):
- """
- See abstract method documentation.
- """
- return self.authenticate(user.email, password, options, debug)[0]
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/customauth/providers/activedirectory.yapsy-plugin
--- a/lib/galaxy/customauth/providers/activedirectory.yapsy-plugin
+++ /dev/null
@@ -1,8 +0,0 @@
-[Core]
-Name = ActiveDirectory
-Module = activedirectory
-
-[Documentation]
-Author = Andrew Robinson
-Version = 0.1
-Description = Custom Authentication Provider that authenticates against an ActiveDirectory (via LDAP). Requires python-ldap module.
\ No newline at end of file
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/customauth/providers/alwaysreject.py
--- a/lib/galaxy/customauth/providers/alwaysreject.py
+++ /dev/null
@@ -1,26 +0,0 @@
-"""
-Created on 16/07/2014
-
-@author: Andrew Robinson
-"""
-
-import galaxy.customauth.base
-
-class AlwaysReject(galaxy.customauth.base.CustomAuthProvider):
- """A simple authenticator that just accepts users (does not care about their
- password).
- """
-
- def authenticate(self, username, password, options, debug=False):
- """
- See abstract method documentation.
- """
- return (None, '')
-
- def authenticateUser(self, user, password, options, debug=False):
- """
- See abstract method documentation.
- """
- if debug:
- print ("User: %s, ALWAYSREJECT: None" % (user.email))
- return None
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/customauth/providers/alwaysreject.yapsy-plugin
--- a/lib/galaxy/customauth/providers/alwaysreject.yapsy-plugin
+++ /dev/null
@@ -1,8 +0,0 @@
-[Core]
-Name = AlwaysReject
-Module = alwaysreject
-
-[Documentation]
-Author = Andrew Robinson
-Version = 0.1
-Description = Custom Authentication Provider that is used for blacklisting usernames (i.e. accept no password)
\ No newline at end of file
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/customauth/providers/localdb.py
--- a/lib/galaxy/customauth/providers/localdb.py
+++ /dev/null
@@ -1,25 +0,0 @@
-"""
-Created on 16/07/2014
-
-@author: Andrew Robinson
-"""
-
-import galaxy.customauth.base
-
-class LocalDB(galaxy.customauth.base.CustomAuthProvider):
- """Authenticate users against the local Galaxy database (as per usual)."""
-
- def authenticate(self, username, password, options, debug=False):
- """
- See abstract method documentation.
- """
- return (False, '') # it can never auto-create based of localdb (chicken-egg)
-
- def authenticateUser(self, user, password, options, debug=False):
- """
- See abstract method documentation.
- """
- user_ok = user.check_password(password)
- if debug:
- print ("User: %s, LOCALDB: %s" % (user.email, user_ok))
- return user_ok
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/customauth/providers/localdb.yapsy-plugin
--- a/lib/galaxy/customauth/providers/localdb.yapsy-plugin
+++ /dev/null
@@ -1,8 +0,0 @@
-[Core]
-Name = LocalDB
-Module = localdb
-
-[Documentation]
-Author = Andrew Robinson
-Version = 0.1
-Description = Custom Authentication Provider that checks against the local database as per normal.
\ No newline at end of file
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/webapps/galaxy/api/authenticate.py
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -18,7 +18,7 @@
from galaxy.managers import api_keys
from galaxy import exceptions
from galaxy.web.base.controller import BaseAPIController
-import galaxy.customauth
+import galaxy.auth
import logging
log = logging.getLogger( __name__ )
@@ -53,7 +53,7 @@
raise exceptions.InconsistentDatabase( 'An error occured, please contact your administrator.' )
else:
user = user[0]
- is_valid_user = galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
+ is_valid_user = galaxy.auth.check_password(user, password, trans.app.config.auth_config_file, trans.app.config.auth_debug)
if is_valid_user:
key = self.api_keys_manager.get_or_create_api_key( user )
return dict( api_key=key )
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/webapps/galaxy/controllers/mobile.py
--- a/lib/galaxy/webapps/galaxy/controllers/mobile.py
+++ b/lib/galaxy/webapps/galaxy/controllers/mobile.py
@@ -1,7 +1,7 @@
from galaxy import web
from galaxy.web.base.controller import *
-import galaxy.customauth
+import galaxy.auth
class Mobile( BaseUIController ):
@@ -59,7 +59,7 @@
# error = password_error = None
# user = trans.sa_session.query( model.User ).filter_by( email = email ).first()
# if not user:
- # autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
+ # autoreg = galaxy.auth.check_auto_registration(trans, email, password, trans.app.config.auth_config_file, trans.app.config.auth_debug)
# if autoreg[0]:
# kwd = {}
# kwd['username'] = autoreg[1]
@@ -83,7 +83,7 @@
# error = "This account has been marked deleted, contact your Galaxy administrator to restore the account."
# elif user.external:
# error = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it."
- # elif not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug):
+ # elif not galaxy.auth.check_password(user, password, trans.app.config.auth_config_file, trans.app.config.auth_debug):
# error = "Invalid password"
# else:
# trans.handle_user_login( user )
diff -r 868d69d100d2aa855df35efb91ba418fef6491dd -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -28,7 +28,7 @@
UsesFormDefinitionsMixin)
from galaxy.web.form_builder import build_select_field, CheckboxField
from galaxy.web.framework.helpers import escape, grids, time_ago
-import galaxy.customauth
+import galaxy.auth
log = logging.getLogger( __name__ )
@@ -514,11 +514,11 @@
redirect = kwd.get( 'redirect', trans.request.referer ).strip()
success = False
user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first()
- if trans.app.config.customauth_debug:
- print ("trans.app.config.customauth_config_file: %s" % trans.app.config.customauth_config_file)
- print ("trans.app.config.customauth_debug: %s WARNING: don't use in production" % trans.app.config.customauth_debug)
+ if trans.app.config.auth_debug:
+ print ("trans.app.config.auth_config_file: %s" % trans.app.config.auth_config_file)
+ print ("trans.app.config.auth_debug: %s WARNING: don't use in production" % trans.app.config.auth_debug)
if not user:
- autoreg = galaxy.customauth.check_auto_registration(trans, email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
+ autoreg = galaxy.auth.check_auto_registration(trans, email, password, trans.app.config.auth_config_file, trans.app.config.auth_debug)
if autoreg[0]:
kwd['username'] = autoreg[1]
params = util.Params( kwd )
@@ -545,7 +545,7 @@
message = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it."
if trans.app.config.error_email_to is not None:
message += ' Contact: %s' % trans.app.config.error_email_to
- elif not galaxy.customauth.check_password(user, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug):
+ elif not galaxy.auth.check_password(user, password, trans.app.config.auth_config_file, trans.app.config.auth_debug):
message = "Invalid password"
elif trans.app.config.user_activation_on and not user.active: # activation is ON and the user is INACTIVE
if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON
@@ -674,7 +674,7 @@
status = 'error'
else:
# check user is allowed to register
- message, status = galaxy.customauth.check_registration_allowed(email, password, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
+ message, status = galaxy.auth.check_registration_allowed(email, password, trans.app.config.auth_config_file, trans.app.config.auth_debug)
if message == '':
if not refresh_frames:
if trans.webapp.name == 'galaxy':
@@ -1125,7 +1125,7 @@
return trans.show_error_message("Invalid or expired password reset token, please request a new one.")
else:
# The user is changing their own password, validate their current password
- (ok, message) = galaxy.customauth.check_change_password(trans.user, current, trans.app.config.customauth_config_file, trans.app.config.customauth_debug)
+ (ok, message) = galaxy.auth.check_change_password(trans.user, current, trans.app.config.auth_config_file, trans.app.config.auth_debug)
if ok:
user = trans.user
else:
https://bitbucket.org/galaxy/galaxy-central/commits/74fcdbccf5a7/
Changeset: 74fcdbccf5a7
User: nsoranzo
Date: 2015-02-24 23:06:25+00:00
Summary: WIP: Initial work on yapsy removal from galaxy.auth .
Affected #: 8 files
diff -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 -r 74fcdbccf5a79b51dc1e30f30eb0aabcc5484f6e lib/galaxy/auth/base.py
--- a/lib/galaxy/auth/base.py
+++ /dev/null
@@ -1,54 +0,0 @@
-"""
-Created on 15/07/2014
-
-@author: Andrew Robinson
-"""
-
-from yapsy.IPlugin import IPlugin
-
-class AuthProvider(IPlugin):
- """A base class for all Auth Providers."""
-
- def authenticate(self, username, password, options, debug=False):
- """
- Check that the username and password are correct.
-
- NOTE: Used within auto-registration to check it is ok to register this
- user.
-
- :param username: the users email address
- :type username: str
- :param password: the plain text password they typed
- :type password: str
- :param options: options provided in auth_config_file
- :type options: dict
- :param debug: whether to print debugging info (defaults to False)
- :type debug: bool
- :returns: True: accept user, False: reject user and None: reject user
- and don't try any other providers. str is the username to register
- with if accepting
- :rtype: (bool, str)
- """
- raise NotImplementedError()
-
- def authenticateUser(self, user, password, options, debug=False):
- """
- Same as authenticate() method, except an User object is provided instead
- of a username.
-
- NOTE: used on normal login to check authentication and update user
- details if required.
-
- :param username: the users email address
- :type username: str
- :param password: the plain text password they typed
- :type password: str
- :param options: options provided in auth_config_file
- :type options: dict
- :param debug: whether to print debugging info (defaults to False)
- :type debug: bool
- :returns: True: accept user, False: reject user and None: reject user
- and don't try any other providers
- :rtype: bool
- """
- raise NotImplementedError()
diff -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 -r 74fcdbccf5a79b51dc1e30f30eb0aabcc5484f6e lib/galaxy/auth/providers/__init__.py
--- a/lib/galaxy/auth/providers/__init__.py
+++ b/lib/galaxy/auth/providers/__init__.py
@@ -0,0 +1,59 @@
+"""
+Created on 15/07/2014
+
+@author: Andrew Robinson
+"""
+
+import abc
+
+class AuthProvider(object):
+ """A base class for all Auth Providers."""
+ __metaclass__ = abc.ABCMeta
+
+ @abc.abstractproperty
+ def plugin_type(self):
+ """ Short string providing labelling this plugin """
+
+ @abc.abstractmethod
+ def authenticate(self, username, password, options, debug=False):
+ """
+ Check that the username and password are correct.
+
+ NOTE: Used within auto-registration to check it is ok to register this
+ user.
+
+ :param username: the users email address
+ :type username: str
+ :param password: the plain text password they typed
+ :type password: str
+ :param options: options provided in auth_config_file
+ :type options: dict
+ :param debug: whether to print debugging info (defaults to False)
+ :type debug: bool
+ :returns: True: accept user, False: reject user and None: reject user
+ and don't try any other providers. str is the username to register
+ with if accepting
+ :rtype: (bool, str)
+ """
+
+ @abc.abstractmethod
+ def authenticateUser(self, user, password, options, debug=False):
+ """
+ Same as authenticate() method, except an User object is provided instead
+ of a username.
+
+ NOTE: used on normal login to check authentication and update user
+ details if required.
+
+ :param username: the users email address
+ :type username: str
+ :param password: the plain text password they typed
+ :type password: str
+ :param options: options provided in auth_config_file
+ :type options: dict
+ :param debug: whether to print debugging info (defaults to False)
+ :type debug: bool
+ :returns: True: accept user, False: reject user and None: reject user
+ and don't try any other providers
+ :rtype: bool
+ """
diff -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 -r 74fcdbccf5a79b51dc1e30f30eb0aabcc5484f6e lib/galaxy/auth/providers/activedirectory.py
--- a/lib/galaxy/auth/providers/activedirectory.py
+++ b/lib/galaxy/auth/providers/activedirectory.py
@@ -5,7 +5,7 @@
"""
import traceback
-import galaxy.auth.base
+from ..providers import AuthProvider
def _getsubs(d, k, vars, default=''):
@@ -14,7 +14,7 @@
return str(default).format(**vars)
-class ActiveDirectory(galaxy.auth.base.AuthProvider):
+class ActiveDirectory(AuthProvider):
"""
Attempts to authenticate users against an Active Directory server.
@@ -22,6 +22,9 @@
those fields first. After that it will bind to the AD with the username
(formatted as specified).
"""
+ @property
+ def plugin_type(self):
+ return 'activedirectory'
def authenticate(self, username, password, options, debug=False):
"""
@@ -48,18 +51,18 @@
try:
# setup connection
ldap.set_option(ldap.OPT_REFERRALS, 0)
- l = ldap.initialize(_getsubs(options,'server',vars))
+ l = ldap.initialize(_getsubs(options, 'server', vars))
l.protocol_version = 3
- l.simple_bind_s(_getsubs(options,'search-user',vars), _getsubs(options,'search-password',vars))
+ l.simple_bind_s(_getsubs(options, 'search-user', vars), _getsubs(options, 'search-password', vars))
scope = ldap.SCOPE_SUBTREE
# setup search
attributes = map(lambda s: s.strip().format(**vars), options['search-fields'].split(','))
- result = l.search(_getsubs(options,'search-base',vars), scope, _getsubs(options,'search-filter',vars), attributes)
+ result = l.search(_getsubs(options, 'search-base', vars), scope, _getsubs(options, 'search-filter', vars), attributes)
# parse results
- _,suser = l.result(result,60)
- _,attrs = suser[0]
+ _, suser = l.result(result, 60)
+ _, attrs = suser[0]
if debug:
print ("AD Search attributes: %s" % attrs)
if hasattr(attrs, 'has_key'):
@@ -78,20 +81,23 @@
try:
# setup connection
ldap.set_option(ldap.OPT_REFERRALS, 0)
- l = ldap.initialize(_getsubs(options,'server',vars))
+ l = ldap.initialize(_getsubs(options, 'server', vars))
l.protocol_version = 3
- l.simple_bind_s(_getsubs(options,'bind-user',vars), _getsubs(options,'bind-password',vars))
+ l.simple_bind_s(_getsubs(options, 'bind-user', vars), _getsubs(options, 'bind-password', vars))
except Exception:
if debug:
- print('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc(),))
+ print('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc()))
return (failuremode, '')
if debug:
print "User: %s, ACTIVEDIRECTORY: True" % (username)
- return (True, _getsubs(options,'auto-register-username',vars))
+ return (True, _getsubs(options, 'auto-register-username', vars))
def authenticateUser(self, user, password, options, debug=False):
"""
See abstract method documentation.
"""
return self.authenticate(user.email, password, options, debug)[0]
+
+
+__all__ = ['ActiveDirectory']
diff -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 -r 74fcdbccf5a79b51dc1e30f30eb0aabcc5484f6e lib/galaxy/auth/providers/activedirectory.yapsy-plugin
--- a/lib/galaxy/auth/providers/activedirectory.yapsy-plugin
+++ /dev/null
@@ -1,8 +0,0 @@
-[Core]
-Name = ActiveDirectory
-Module = activedirectory
-
-[Documentation]
-Author = Andrew Robinson
-Version = 0.1
-Description = Authentication Provider that authenticates against an ActiveDirectory (via LDAP). Requires python-ldap module.
diff -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 -r 74fcdbccf5a79b51dc1e30f30eb0aabcc5484f6e lib/galaxy/auth/providers/alwaysreject.py
--- a/lib/galaxy/auth/providers/alwaysreject.py
+++ b/lib/galaxy/auth/providers/alwaysreject.py
@@ -4,12 +4,16 @@
@author: Andrew Robinson
"""
-import galaxy.auth.base
+from ..providers import AuthProvider
-class AlwaysReject(galaxy.auth.base.AuthProvider):
+
+class AlwaysReject(AuthProvider):
"""A simple authenticator that just accepts users (does not care about their
password).
"""
+ @property
+ def plugin_type(self):
+ return 'alwaysreject'
def authenticate(self, username, password, options, debug=False):
"""
@@ -24,3 +28,6 @@
if debug:
print ("User: %s, ALWAYSREJECT: None" % (user.email))
return None
+
+
+__all__ = ['AlwaysReject']
diff -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 -r 74fcdbccf5a79b51dc1e30f30eb0aabcc5484f6e lib/galaxy/auth/providers/alwaysreject.yapsy-plugin
--- a/lib/galaxy/auth/providers/alwaysreject.yapsy-plugin
+++ /dev/null
@@ -1,8 +0,0 @@
-[Core]
-Name = AlwaysReject
-Module = alwaysreject
-
-[Documentation]
-Author = Andrew Robinson
-Version = 0.1
-Description = Authentication Provider that is used for blacklisting usernames (i.e. accept no password)
diff -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 -r 74fcdbccf5a79b51dc1e30f30eb0aabcc5484f6e lib/galaxy/auth/providers/localdb.py
--- a/lib/galaxy/auth/providers/localdb.py
+++ b/lib/galaxy/auth/providers/localdb.py
@@ -4,10 +4,14 @@
@author: Andrew Robinson
"""
-import galaxy.auth.base
+from ..providers import AuthProvider
-class LocalDB(galaxy.auth.base.AuthProvider):
+
+class LocalDB(AuthProvider):
"""Authenticate users against the local Galaxy database (as per usual)."""
+ @property
+ def plugin_type(self):
+ return 'localdb'
def authenticate(self, username, password, options, debug=False):
"""
@@ -23,3 +27,6 @@
if debug:
print ("User: %s, LOCALDB: %s" % (user.email, user_ok))
return user_ok
+
+
+__all__ = ['LocalDB']
diff -r 8d0ea77d02b404a17a4c2e058f4b537bf7a05ba0 -r 74fcdbccf5a79b51dc1e30f30eb0aabcc5484f6e lib/galaxy/auth/providers/localdb.yapsy-plugin
--- a/lib/galaxy/auth/providers/localdb.yapsy-plugin
+++ /dev/null
@@ -1,8 +0,0 @@
-[Core]
-Name = LocalDB
-Module = localdb
-
-[Documentation]
-Author = Andrew Robinson
-Version = 0.1
-Description = Authentication Provider that checks against the local database as per normal.
https://bitbucket.org/galaxy/galaxy-central/commits/dd0d3b4df70f/
Changeset: dd0d3b4df70f
User: jmchilton
Date: 2015-03-02 01:08:29+00:00
Summary: Use galaxy-style logging instead of print in galaxy.auth.
Affected #: 1 file
diff -r 74fcdbccf5a79b51dc1e30f30eb0aabcc5484f6e -r dd0d3b4df70ff7c0dae880cd7488aeec42af7878 lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -9,7 +9,7 @@
from galaxy.security.validate_user_input import validate_publicname
import logging
-logging.basicConfig(level=logging.DEBUG)
+log = logging.getLogger(__name__)
# <auth>
# <authenticator>
@@ -61,7 +61,7 @@
for provider, options in activeAuthProviderGenerator(email, password, configfile, debug):
if provider is None:
if debug:
- print "Unable to find module: %s" % options
+ log.debug( "Unable to find module: %s" % options )
else:
authresult, autousername = provider.authenticate(email, password, options, debug)
autousername = str(autousername).lower()
@@ -77,10 +77,10 @@
else:
break # end for loop if we can't make a unique username
if debug:
- print "Email: %s, auto-register with username: %s" % (email, autousername)
+ log.debug( "Email: %s, auto-register with username: %s" % (email, autousername) )
return (_getBool(options, 'auto-register', False), autousername)
elif authresult is None:
- print "Email: %s, stopping due to failed non-continue" % (email)
+ log.debug( "Email: %s, stopping due to failed non-continue" % (email) )
break # end authentication (skip rest)
return (False, '')
@@ -89,7 +89,7 @@
for provider, options in activeAuthProviderGenerator(user.email, password, configfile, debug):
if provider is None:
if debug:
- print "Unable to find module: %s" % options
+ log.debug( "Unable to find module: %s" % options )
else:
authresult = provider.authenticateUser(user, password, options, debug)
if authresult is True:
@@ -105,7 +105,7 @@
for provider, options in activeAuthProviderGenerator(user.email, current_password, configfile, debug):
if provider is None:
if debug:
- print "Unable to find module: %s" % options
+ log.debug( "Unable to find module: %s" % options )
else:
if _getBool(options, "allow-password-change", False):
authresult = provider.authenticateUser(user, current_password, options, debug)
@@ -128,9 +128,9 @@
manager.collectPlugins()
if debug:
- print ("Plugins found:")
+ log.debug( ("Plugins found:") )
for plugin in manager.getAllPlugins():
- print ("- %s" % (plugin.path))
+ log.debug( ("- %s" % (plugin.path)) )
# parse XML
ct = xml.etree.ElementTree.parse(configfile)
@@ -145,7 +145,7 @@
if filterelem is not None:
filterstr = str(filterelem.text).format(username=username, password=password)
if debug:
- print ("Filter: %s == %s" % (filterstr, eval(filterstr, {"__builtins__":None},{'str':str})))
+ log.debug( ("Filter: %s == %s" % (filterstr, eval(filterstr, {"__builtins__":None},{'str':str}))) )
if not eval(filterstr, {"__builtins__":None},{'str':str}):
continue # skip to next
@@ -163,7 +163,7 @@
return
except:
if debug:
- print ('Auth: Exception:\n%s' % (traceback.format_exc(),))
+ log.debug( ('Auth: Exception:\n%s' % (traceback.format_exc(),)) )
def _getBool(d, k, o):
if k in d:
https://bitbucket.org/galaxy/galaxy-central/commits/56d21c8237db/
Changeset: 56d21c8237db
User: jmchilton
Date: 2015-03-02 01:11:14+00:00
Summary: Reuse galaxy.util bool checking in galaxy.auth.
Affected #: 1 file
diff -r dd0d3b4df70ff7c0dae880cd7488aeec42af7878 -r 56d21c8237dbd121825ec79c6f0b476e1374ac7e lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -8,6 +8,11 @@
from galaxy.security.validate_user_input import validate_publicname
+from galaxy.util import (
+ string_as_bool,
+ string_as_bool_or_none,
+)
+
import logging
log = logging.getLogger(__name__)
@@ -167,21 +172,13 @@
def _getBool(d, k, o):
if k in d:
- if d[k] in ('True', 'true', 'Yes', 'yes', '1', 1, True):
- return True
- else:
- return False
+ return string_as_bool(d[k])
else:
return o
def _getTriState(d, k, o):
if k in d:
- if d[k] in ('True', 'true', 'Yes', 'yes', '1', 1, True):
- return True
- elif d[k] in ('False', 'false', 'No', 'no', '0', 0, False):
- return False
- else:
- return None
+ return string_as_bool_or_none(d[k])
else:
return o
https://bitbucket.org/galaxy/galaxy-central/commits/a47c91afe317/
Changeset: a47c91afe317
User: jmchilton
Date: 2015-03-02 01:17:11+00:00
Summary: PEP-8 fixes for auth code.
Affected #: 4 files
diff -r 56d21c8237dbd121825ec79c6f0b476e1374ac7e -r a47c91afe31716b7a4dd527fc32804fab305989b lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -36,15 +36,16 @@
# ...
# </auth>
+
def check_registration_allowed(email, password, configfile, debug=False):
"""Checks if the provided email is allowed to register."""
message = ''
status = 'done'
for provider, options in activeAuthProviderGenerator(email, password, configfile, debug):
allowreg = _getTriState(options, 'allow-register', True)
- if allowreg is None: # i.e. challenge
+ if allowreg is None: # i.e. challenge
authresult, msg = provider.authenticate(email, password, options, debug)
- if authresult == True:
+ if authresult is True:
break
if authresult is None:
message = 'Invalid email address or password'
@@ -58,6 +59,7 @@
break
return message, status
+
def check_auto_registration(trans, email, password, configfile, debug=False):
"""
Checks the email/password using auth providers in order. If a match is
@@ -74,21 +76,22 @@
# make username unique
if validate_publicname( trans, autousername ) != '':
i = 1
- while i <= 10: # stop after 10 tries
+ while i <= 10: # stop after 10 tries
if validate_publicname( trans, "%s-%i" % (autousername, i) ) == '':
autousername = "%s-%i" % (autousername, i)
break
i += 1
else:
- break # end for loop if we can't make a unique username
+ break # end for loop if we can't make a unique username
if debug:
log.debug( "Email: %s, auto-register with username: %s" % (email, autousername) )
return (_getBool(options, 'auto-register', False), autousername)
elif authresult is None:
log.debug( "Email: %s, stopping due to failed non-continue" % (email) )
- break # end authentication (skip rest)
+ break # end authentication (skip rest)
return (False, '')
+
def check_password(user, password, configfile, debug=False):
"""Checks the email/password using auth providers."""
for provider, options in activeAuthProviderGenerator(user.email, password, configfile, debug):
@@ -98,11 +101,12 @@
else:
authresult = provider.authenticateUser(user, password, options, debug)
if authresult is True:
- return True # accept user
+ return True # accept user
elif authresult is None:
- break # end authentication (skip rest)
+ break # end authentication (skip rest)
return False
+
def check_change_password(user, current_password, configfile, debug=False):
"""Checks that auth provider allows password changes and current_password
matches.
@@ -115,13 +119,14 @@
if _getBool(options, "allow-password-change", False):
authresult = provider.authenticateUser(user, current_password, options, debug)
if authresult is True:
- return (True, '') # accept user
+ return (True, '') # accept user
elif authresult is None:
- break # end authentication (skip rest)
+ break # end authentication (skip rest)
else:
return (False, 'Password change not supported')
return (False, 'Invalid current password')
+
def activeAuthProviderGenerator(username, password, configfile, debug):
"""Yields AuthProvider instances for the provided configfile that match the
filters.
@@ -150,9 +155,9 @@
if filterelem is not None:
filterstr = str(filterelem.text).format(username=username, password=password)
if debug:
- log.debug( ("Filter: %s == %s" % (filterstr, eval(filterstr, {"__builtins__":None},{'str':str}))) )
- if not eval(filterstr, {"__builtins__":None},{'str':str}):
- continue # skip to next
+ log.debug( ("Filter: %s == %s" % (filterstr, eval(filterstr, {"__builtins__": None}, {'str': str}))) )
+ if not eval(filterstr, {"__builtins__": None}, {'str': str}):
+ continue # skip to next
# extract options
optionselem = _getChildElement(authelem, 'options')
@@ -170,18 +175,21 @@
if debug:
log.debug( ('Auth: Exception:\n%s' % (traceback.format_exc(),)) )
+
def _getBool(d, k, o):
if k in d:
return string_as_bool(d[k])
else:
return o
+
def _getTriState(d, k, o):
if k in d:
return string_as_bool_or_none(d[k])
else:
return o
+
def _getChildElement(parent, childname):
try:
return parent.iter(childname).next()
diff -r 56d21c8237dbd121825ec79c6f0b476e1374ac7e -r a47c91afe31716b7a4dd527fc32804fab305989b lib/galaxy/auth/providers/__init__.py
--- a/lib/galaxy/auth/providers/__init__.py
+++ b/lib/galaxy/auth/providers/__init__.py
@@ -6,6 +6,7 @@
import abc
+
class AuthProvider(object):
"""A base class for all Auth Providers."""
__metaclass__ = abc.ABCMeta
diff -r 56d21c8237dbd121825ec79c6f0b476e1374ac7e -r a47c91afe31716b7a4dd527fc32804fab305989b lib/galaxy/auth/providers/activedirectory.py
--- a/lib/galaxy/auth/providers/activedirectory.py
+++ b/lib/galaxy/auth/providers/activedirectory.py
@@ -34,9 +34,9 @@
print ("Username: %s" % username)
print ("Options: %s" % options)
- failuremode = False # reject but continue
+ failuremode = False # reject but continue
if options.get('continue-on-failure', 'False') == 'False':
- failuremode = None # reject and do not continue
+ failuremode = None # reject and do not continue
try:
import ldap
@@ -45,7 +45,7 @@
print ("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
return (failuremode, '')
- ## do AD search (if required) ##
+ # do AD search (if required)
vars = {'username': username, 'password': password}
if 'search-fields' in options:
try:
@@ -67,7 +67,7 @@
print ("AD Search attributes: %s" % attrs)
if hasattr(attrs, 'has_key'):
for attr in attributes:
- if attrs.has_key(attr):
+ if attr in attrs:
vars[attr] = str(attrs[attr][0])
else:
vars[attr] = ""
diff -r 56d21c8237dbd121825ec79c6f0b476e1374ac7e -r a47c91afe31716b7a4dd527fc32804fab305989b lib/galaxy/auth/providers/localdb.py
--- a/lib/galaxy/auth/providers/localdb.py
+++ b/lib/galaxy/auth/providers/localdb.py
@@ -17,7 +17,7 @@
"""
See abstract method documentation.
"""
- return (False, '') # it can never auto-create based of localdb (chicken-egg)
+ return (False, '') # it can never auto-create based of localdb (chicken-egg)
def authenticateUser(self, user, password, options, debug=False):
"""
https://bitbucket.org/galaxy/galaxy-central/commits/e3aa33dfb08e/
Changeset: e3aa33dfb08e
User: jmchilton
Date: 2015-03-02 01:18:40+00:00
Summary: Finish replacing YAPSY with galaxy.util.plugin_config.
Affected #: 1 file
diff -r a47c91afe31716b7a4dd527fc32804fab305989b -r e3aa33dfb08e8a287a69f695e862ec89c646d04d lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -4,7 +4,6 @@
import traceback
import xml.etree.ElementTree
-from yapsy.PluginManager import PluginManager
from galaxy.security.validate_user_input import validate_publicname
@@ -13,6 +12,9 @@
string_as_bool_or_none,
)
+from galaxy.util import plugin_config
+
+
import logging
log = logging.getLogger(__name__)
@@ -132,15 +134,13 @@
filters.
"""
try:
- # load the yapsy plugins
- manager = PluginManager()
- manager.setPluginPlaces(["lib/galaxy/auth/providers"])
- manager.collectPlugins()
+ import galaxy.auth.providers
+ plugins_dict = plugin_config.plugins_dict( galaxy.auth.providers, 'plugin_type' )
if debug:
log.debug( ("Plugins found:") )
- for plugin in manager.getAllPlugins():
- log.debug( ("- %s" % (plugin.path)) )
+ for plugin in plugins_dict:
+ log.debug( ("- %s" % (plugin)) )
# parse XML
ct = xml.etree.ElementTree.parse(configfile)
@@ -167,7 +167,7 @@
options[opt.tag] = opt.text
# get the instance
- plugin = manager.getPluginByName(typeelem.text)
+ plugin = plugins_dict.get(typeelem.text)
yield (plugin.plugin_object, options) # excepts if type is spelled incorrectly
except GeneratorExit:
return
https://bitbucket.org/galaxy/galaxy-central/commits/9562cb4c7b7d/
Changeset: 9562cb4c7b7d
User: jmchilton
Date: 2015-03-02 01:56:53+00:00
Summary: Rearrange auth to use a Galaxy manager object pattern.
On the positive-side this feels much more like a traditional Galaxy style access pattern and each operation is likely much more efficient since the plugins aren't be reloaded and XML re-parsed for each action. The downside is a Galaxy restart is required to update the authentication providers for Galaxy - while this is less than ideal in some ways - it is what Galaxy admins would expect for the other configuration files anyway so it is arguably better to not be more clever here.
Affected #: 7 files
diff -r e3aa33dfb08e8a287a69f695e862ec89c646d04d -r 9562cb4c7b7dc4e75465c9bf26b8c322cc2b8342 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -120,6 +120,8 @@
else:
self.openid_providers = OpenIDProviders()
# Start the heartbeat process if configured and available
+ from galaxy import auth
+ self.auth_manager = auth.AuthManager( self )
if self.config.use_heartbeat:
from galaxy.util import heartbeat
if heartbeat.Heartbeat:
diff -r e3aa33dfb08e8a287a69f695e862ec89c646d04d -r 9562cb4c7b7dc4e75465c9bf26b8c322cc2b8342 lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -2,6 +2,7 @@
Contains implementations of the authentication logic.
"""
+from collections import namedtuple
import traceback
import xml.etree.ElementTree
@@ -39,125 +40,33 @@
# </auth>
-def check_registration_allowed(email, password, configfile, debug=False):
- """Checks if the provided email is allowed to register."""
- message = ''
- status = 'done'
- for provider, options in activeAuthProviderGenerator(email, password, configfile, debug):
- allowreg = _getTriState(options, 'allow-register', True)
- if allowreg is None: # i.e. challenge
- authresult, msg = provider.authenticate(email, password, options, debug)
- if authresult is True:
- break
- if authresult is None:
- message = 'Invalid email address or password'
- status = 'error'
- break
- elif allowreg is True:
- break
- elif allowreg is False:
- message = 'Account registration not required for your account. Please simply login.'
- status = 'error'
- break
- return message, status
+class AuthManager(object):
+ def __init__(self, app):
+ self.__app = app
+ import galaxy.auth.providers
+ self.__plugins_dict = plugin_config.plugins_dict( galaxy.auth.providers, 'plugin_type' )
+ auth_config_file = app.config.auth_config_file
+ self.__init_authenticators(auth_config_file)
+ self.debug = getattr(app.config, 'auth_debug', False)
-def check_auto_registration(trans, email, password, configfile, debug=False):
- """
- Checks the email/password using auth providers in order. If a match is
- found, returns the 'auto-register' option for that provider.
- """
- for provider, options in activeAuthProviderGenerator(email, password, configfile, debug):
- if provider is None:
- if debug:
- log.debug( "Unable to find module: %s" % options )
- else:
- authresult, autousername = provider.authenticate(email, password, options, debug)
- autousername = str(autousername).lower()
- if authresult is True:
- # make username unique
- if validate_publicname( trans, autousername ) != '':
- i = 1
- while i <= 10: # stop after 10 tries
- if validate_publicname( trans, "%s-%i" % (autousername, i) ) == '':
- autousername = "%s-%i" % (autousername, i)
- break
- i += 1
- else:
- break # end for loop if we can't make a unique username
- if debug:
- log.debug( "Email: %s, auto-register with username: %s" % (email, autousername) )
- return (_getBool(options, 'auto-register', False), autousername)
- elif authresult is None:
- log.debug( "Email: %s, stopping due to failed non-continue" % (email) )
- break # end authentication (skip rest)
- return (False, '')
-
-
-def check_password(user, password, configfile, debug=False):
- """Checks the email/password using auth providers."""
- for provider, options in activeAuthProviderGenerator(user.email, password, configfile, debug):
- if provider is None:
- if debug:
- log.debug( "Unable to find module: %s" % options )
- else:
- authresult = provider.authenticateUser(user, password, options, debug)
- if authresult is True:
- return True # accept user
- elif authresult is None:
- break # end authentication (skip rest)
- return False
-
-
-def check_change_password(user, current_password, configfile, debug=False):
- """Checks that auth provider allows password changes and current_password
- matches.
- """
- for provider, options in activeAuthProviderGenerator(user.email, current_password, configfile, debug):
- if provider is None:
- if debug:
- log.debug( "Unable to find module: %s" % options )
- else:
- if _getBool(options, "allow-password-change", False):
- authresult = provider.authenticateUser(user, current_password, options, debug)
- if authresult is True:
- return (True, '') # accept user
- elif authresult is None:
- break # end authentication (skip rest)
- else:
- return (False, 'Password change not supported')
- return (False, 'Invalid current password')
-
-
-def activeAuthProviderGenerator(username, password, configfile, debug):
- """Yields AuthProvider instances for the provided configfile that match the
- filters.
- """
- try:
- import galaxy.auth.providers
- plugins_dict = plugin_config.plugins_dict( galaxy.auth.providers, 'plugin_type' )
-
- if debug:
- log.debug( ("Plugins found:") )
- for plugin in plugins_dict:
- log.debug( ("- %s" % (plugin)) )
-
+ def __init_authenticators(self, auth_config_file):
# parse XML
- ct = xml.etree.ElementTree.parse(configfile)
+ ct = xml.etree.ElementTree.parse(auth_config_file)
confroot = ct.getroot()
+ authenticators = []
# process authenticators
for authelem in confroot.getchildren():
typeelem = authelem.iter('type').next()
+ plugin = self.__plugins_dict.get(typeelem.text)
# check filterelem
- filterelem = _getChildElement(authelem, 'filter')
- if filterelem is not None:
- filterstr = str(filterelem.text).format(username=username, password=password)
- if debug:
- log.debug( ("Filter: %s == %s" % (filterstr, eval(filterstr, {"__builtins__": None}, {'str': str}))) )
- if not eval(filterstr, {"__builtins__": None}, {'str': str}):
- continue # skip to next
+ filter_elem = _getChildElement(authelem, 'filter')
+ if filter_elem is not None:
+ filter_template = str(filter_elem.text)
+ else:
+ filter_template = None
# extract options
optionselem = _getChildElement(authelem, 'options')
@@ -165,15 +74,118 @@
if optionselem is not None:
for opt in optionselem:
options[opt.tag] = opt.text
+ authenticator = Authenticator(
+ plugin=plugin,
+ filter_template=filter_template,
+ options=options,
+ )
+ authenticators.append(authenticator)
+ self.authenticators = authenticators
- # get the instance
- plugin = plugins_dict.get(typeelem.text)
- yield (plugin.plugin_object, options) # excepts if type is spelled incorrectly
- except GeneratorExit:
- return
- except:
- if debug:
- log.debug( ('Auth: Exception:\n%s' % (traceback.format_exc(),)) )
+ def check_registration_allowed(self, email, password):
+ """Checks if the provided email is allowed to register."""
+ message = ''
+ status = 'done'
+ for provider, options in self.activeAuthProviderGenerator(email, password):
+ allowreg = _getTriState(options, 'allow-register', True)
+ if allowreg is None: # i.e. challenge
+ authresult, msg = provider.authenticate(email, password, options)
+ if authresult is True:
+ break
+ if authresult is None:
+ message = 'Invalid email address or password'
+ status = 'error'
+ break
+ elif allowreg is True:
+ break
+ elif allowreg is False:
+ message = 'Account registration not required for your account. Please simply login.'
+ status = 'error'
+ break
+ return message, status
+
+ def check_auto_registration(self, trans, email, password, debug=False):
+ """
+ Checks the email/password using auth providers in order. If a match is
+ found, returns the 'auto-register' option for that provider.
+ """
+ for provider, options in self.activeAuthProviderGenerator(email, password, debug):
+ if provider is None:
+ if debug:
+ log.debug( "Unable to find module: %s" % options )
+ else:
+ authresult, autousername = provider.authenticate(email, password, options, debug)
+ autousername = str(autousername).lower()
+ if authresult is True:
+ # make username unique
+ if validate_publicname( trans, autousername ) != '':
+ i = 1
+ while i <= 10: # stop after 10 tries
+ if validate_publicname( trans, "%s-%i" % (autousername, i) ) == '':
+ autousername = "%s-%i" % (autousername, i)
+ break
+ i += 1
+ else:
+ break # end for loop if we can't make a unique username
+ if debug:
+ log.debug( "Email: %s, auto-register with username: %s" % (email, autousername) )
+ return (_getBool(options, 'auto-register', False), autousername)
+ elif authresult is None:
+ log.debug( "Email: %s, stopping due to failed non-continue" % (email) )
+ break # end authentication (skip rest)
+ return (False, '')
+
+ def check_password(self, user, password):
+ """Checks the email/password using auth providers."""
+ for provider, options in self.activeAuthProviderGenerator(user.email, password):
+ if provider is None:
+ if self.debug:
+ log.debug( "Unable to find module: %s" % options )
+ else:
+ authresult = provider.authenticateUser(user, password, options)
+ if authresult is True:
+ return True # accept user
+ elif authresult is None:
+ break # end authentication (skip rest)
+ return False
+
+ def check_change_password(self, user, current_password):
+ """Checks that auth provider allows password changes and current_password
+ matches.
+ """
+ for provider, options in self.activeAuthProviderGenerator(user.email, current_password):
+ if provider is None:
+ if self.debug:
+ log.debug( "Unable to find module: %s" % options )
+ else:
+ if _getBool(options, "allow-password-change", False):
+ authresult = provider.authenticateUser(user, current_password, options)
+ if authresult is True:
+ return (True, '') # accept user
+ elif authresult is None:
+ break # end authentication (skip rest)
+ else:
+ return (False, 'Password change not supported')
+ return (False, 'Invalid current password')
+
+ def activeAuthProviderGenerator(self, username, password):
+ """Yields AuthProvider instances for the provided configfile that match the
+ filters.
+ """
+ try:
+ for authenticator in self.authenticators:
+ filter_template = authenticator.filter_template
+ if filter_template:
+ filter_str = filter_template.format(username=username, password=password)
+ if not eval(filter_str, {"__builtins__": None}, {'str': str}):
+ continue # skip to next
+ yield authenticator.plugin, authenticator.options
+ except Exception:
+ if self.debug:
+ log.debug( ('Auth: Exception:\n%s' % (traceback.format_exc(),)) )
+ raise
+
+Authenticator = namedtuple('Authenticator', ['plugin', 'filter_template', 'options'])
def _getBool(d, k, o):
diff -r e3aa33dfb08e8a287a69f695e862ec89c646d04d -r 9562cb4c7b7dc4e75465c9bf26b8c322cc2b8342 lib/galaxy/webapps/galaxy/api/authenticate.py
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -18,7 +18,6 @@
from galaxy.managers import api_keys
from galaxy import exceptions
from galaxy.web.base.controller import BaseAPIController
-import galaxy.auth
import logging
log = logging.getLogger( __name__ )
@@ -53,7 +52,7 @@
raise exceptions.InconsistentDatabase( 'An error occured, please contact your administrator.' )
else:
user = user[0]
- is_valid_user = galaxy.auth.check_password(user, password, trans.app.config.auth_config_file, trans.app.config.auth_debug)
+ is_valid_user = self.auth_manager.check_password(user, password)
if is_valid_user:
key = self.api_keys_manager.get_or_create_api_key( user )
return dict( api_key=key )
diff -r e3aa33dfb08e8a287a69f695e862ec89c646d04d -r 9562cb4c7b7dc4e75465c9bf26b8c322cc2b8342 lib/galaxy/webapps/galaxy/controllers/mobile.py
--- a/lib/galaxy/webapps/galaxy/controllers/mobile.py
+++ b/lib/galaxy/webapps/galaxy/controllers/mobile.py
@@ -1,7 +1,6 @@
from galaxy import web
from galaxy.web.base.controller import *
-import galaxy.auth
class Mobile( BaseUIController ):
diff -r e3aa33dfb08e8a287a69f695e862ec89c646d04d -r 9562cb4c7b7dc4e75465c9bf26b8c322cc2b8342 lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -28,7 +28,7 @@
UsesFormDefinitionsMixin)
from galaxy.web.form_builder import build_select_field, CheckboxField
from galaxy.web.framework.helpers import escape, grids, time_ago
-import galaxy.auth
+
log = logging.getLogger( __name__ )
@@ -518,7 +518,7 @@
print ("trans.app.config.auth_config_file: %s" % trans.app.config.auth_config_file)
print ("trans.app.config.auth_debug: %s WARNING: don't use in production" % trans.app.config.auth_debug)
if not user:
- autoreg = galaxy.auth.check_auto_registration(trans, email, password, trans.app.config.auth_config_file, trans.app.config.auth_debug)
+ autoreg = trans.app.auth_manager.check_auto_registration(trans, email, password)
if autoreg[0]:
kwd['username'] = autoreg[1]
params = util.Params( kwd )
@@ -545,7 +545,7 @@
message = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it."
if trans.app.config.error_email_to is not None:
message += ' Contact: %s' % trans.app.config.error_email_to
- elif not galaxy.auth.check_password(user, password, trans.app.config.auth_config_file, trans.app.config.auth_debug):
+ elif not trans.app.auth_manager.check_password(user, password):
message = "Invalid password"
elif trans.app.config.user_activation_on and not user.active: # activation is ON and the user is INACTIVE
if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON
@@ -674,7 +674,7 @@
status = 'error'
else:
# check user is allowed to register
- message, status = galaxy.auth.check_registration_allowed(email, password, trans.app.config.auth_config_file, trans.app.config.auth_debug)
+ message, status = trans.app.auth_manager.check_registration_allowed(email, password)
if message == '':
if not refresh_frames:
if trans.webapp.name == 'galaxy':
@@ -1125,7 +1125,7 @@
return trans.show_error_message("Invalid or expired password reset token, please request a new one.")
else:
# The user is changing their own password, validate their current password
- (ok, message) = galaxy.auth.check_change_password(trans.user, current, trans.app.config.auth_config_file, trans.app.config.auth_debug)
+ (ok, message) = trans.app.auth_manager.check_change_password(trans.user, current )
if ok:
user = trans.user
else:
diff -r e3aa33dfb08e8a287a69f695e862ec89c646d04d -r 9562cb4c7b7dc4e75465c9bf26b8c322cc2b8342 lib/galaxy/webapps/tool_shed/app.py
--- a/lib/galaxy/webapps/tool_shed/app.py
+++ b/lib/galaxy/webapps/tool_shed/app.py
@@ -53,6 +53,8 @@
# because the Tool Shed should always have an empty dictionary!
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path )
self.genome_builds = GenomeBuilds( self )
+ from galaxy import auth
+ self.auth_manager = auth.AuthManager( self )
# Citation manager needed to load tools.
from galaxy.managers.citations import CitationsManager
self.citations_manager = CitationsManager( self )
diff -r e3aa33dfb08e8a287a69f695e862ec89c646d04d -r 9562cb4c7b7dc4e75465c9bf26b8c322cc2b8342 lib/galaxy/webapps/tool_shed/config.py
--- a/lib/galaxy/webapps/tool_shed/config.py
+++ b/lib/galaxy/webapps/tool_shed/config.py
@@ -132,6 +132,7 @@
if global_conf and "__file__" in global_conf:
global_conf_parser.read(global_conf['__file__'])
self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) )
+ self.auth_debug = string_as_bool( kwargs.get( 'auth_debug', False ) )
self.citation_cache_type = kwargs.get( "citation_cache_type", "file" )
self.citation_cache_data_dir = resolve_path( kwargs.get( "citation_cache_data_dir", "database/tool_shed_citations/data" ), self.root )
self.citation_cache_lock_dir = resolve_path( kwargs.get( "citation_cache_lock_dir", "database/tool_shed_citations/locks" ), self.root )
@@ -155,6 +156,7 @@
def __parse_config_file_options( self, kwargs ):
defaults = dict(
+ auth_config_file=[ 'config/auth_conf.xml', 'config/auth_conf.xml.sample' ],
datatypes_config_file = [ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ],
shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ],
)
https://bitbucket.org/galaxy/galaxy-central/commits/1c373ec50827/
Changeset: 1c373ec50827
User: jmchilton
Date: 2015-03-02 02:38:39+00:00
Summary: Default auth provider should allow password change.
Affected #: 1 file
diff -r 9562cb4c7b7dc4e75465c9bf26b8c322cc2b8342 -r 1c373ec50827490069fbff58020bcaf784261959 config/auth_conf.xml.sample
--- a/config/auth_conf.xml.sample
+++ b/config/auth_conf.xml.sample
@@ -1,6 +1,9 @@
<?xml version="1.0"?><auth>
- <authenticator>
- <type>localdb</type>
- </authenticator>
+ <authenticator>
+ <type>localdb</type>
+ <options>
+ <allow-password-change>true</allow-password-change>
+ </options>
+ </authenticator></auth>
https://bitbucket.org/galaxy/galaxy-central/commits/03e964afd157/
Changeset: 03e964afd157
User: jmchilton
Date: 2015-03-02 02:39:23+00:00
Summary: Auth fixes for switch from YAPSY to plugin_config.
Affected #: 4 files
diff -r 1c373ec50827490069fbff58020bcaf784261959 -r 03e964afd1578a1df236e70cbe55659967458028 lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -59,7 +59,7 @@
# process authenticators
for authelem in confroot.getchildren():
typeelem = authelem.iter('type').next()
- plugin = self.__plugins_dict.get(typeelem.text)
+ plugin = self.__plugins_dict.get(typeelem.text)()
# check filterelem
filter_elem = _getChildElement(authelem, 'filter')
@@ -177,7 +177,8 @@
filter_template = authenticator.filter_template
if filter_template:
filter_str = filter_template.format(username=username, password=password)
- if not eval(filter_str, {"__builtins__": None}, {'str': str}):
+ passed_filter = eval(filter_str, {"__builtins__": None}, {'str': str})
+ if not passed_filter:
continue # skip to next
yield authenticator.plugin, authenticator.options
except Exception:
diff -r 1c373ec50827490069fbff58020bcaf784261959 -r 03e964afd1578a1df236e70cbe55659967458028 lib/galaxy/auth/providers/activedirectory.py
--- a/lib/galaxy/auth/providers/activedirectory.py
+++ b/lib/galaxy/auth/providers/activedirectory.py
@@ -22,9 +22,7 @@
those fields first. After that it will bind to the AD with the username
(formatted as specified).
"""
- @property
- def plugin_type(self):
- return 'activedirectory'
+ plugin_type = 'activedirectory'
def authenticate(self, username, password, options, debug=False):
"""
diff -r 1c373ec50827490069fbff58020bcaf784261959 -r 03e964afd1578a1df236e70cbe55659967458028 lib/galaxy/auth/providers/alwaysreject.py
--- a/lib/galaxy/auth/providers/alwaysreject.py
+++ b/lib/galaxy/auth/providers/alwaysreject.py
@@ -11,9 +11,7 @@
"""A simple authenticator that just accepts users (does not care about their
password).
"""
- @property
- def plugin_type(self):
- return 'alwaysreject'
+ plugin_type = 'alwaysreject'
def authenticate(self, username, password, options, debug=False):
"""
diff -r 1c373ec50827490069fbff58020bcaf784261959 -r 03e964afd1578a1df236e70cbe55659967458028 lib/galaxy/auth/providers/localdb.py
--- a/lib/galaxy/auth/providers/localdb.py
+++ b/lib/galaxy/auth/providers/localdb.py
@@ -5,13 +5,13 @@
"""
from ..providers import AuthProvider
+import logging
+log = logging.getLogger(__name__)
class LocalDB(AuthProvider):
"""Authenticate users against the local Galaxy database (as per usual)."""
- @property
- def plugin_type(self):
- return 'localdb'
+ plugin_type = 'localdb'
def authenticate(self, username, password, options, debug=False):
"""
https://bitbucket.org/galaxy/galaxy-central/commits/77ad730cd686/
Changeset: 77ad730cd686
User: jmchilton
Date: 2015-03-02 03:09:34+00:00
Summary: Replace print statements with log statements in auth providers.
This is more galactic.
Affected #: 3 files
diff -r 03e964afd1578a1df236e70cbe55659967458028 -r 77ad730cd6866e89cb8bcad865cacef66a15fd49 lib/galaxy/auth/providers/activedirectory.py
--- a/lib/galaxy/auth/providers/activedirectory.py
+++ b/lib/galaxy/auth/providers/activedirectory.py
@@ -7,6 +7,9 @@
import traceback
from ..providers import AuthProvider
+import logging
+log = logging.getLogger(__name__)
+
def _getsubs(d, k, vars, default=''):
if k in d:
@@ -29,8 +32,8 @@
See abstract method documentation.
"""
if debug:
- print ("Username: %s" % username)
- print ("Options: %s" % options)
+ log.debug("Username: %s" % username)
+ log.debug("Options: %s" % options)
failuremode = False # reject but continue
if options.get('continue-on-failure', 'False') == 'False':
@@ -40,7 +43,7 @@
import ldap
except:
if debug:
- print ("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
+ log.debug("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
return (failuremode, '')
# do AD search (if required)
@@ -62,7 +65,7 @@
_, suser = l.result(result, 60)
_, attrs = suser[0]
if debug:
- print ("AD Search attributes: %s" % attrs)
+ log.debug(("AD Search attributes: %s" % attrs))
if hasattr(attrs, 'has_key'):
for attr in attributes:
if attr in attrs:
@@ -71,7 +74,7 @@
vars[attr] = ""
except Exception:
if debug:
- print('User: %s, ACTIVEDIRECTORY: Search Exception:\n%s' % (username, traceback.format_exc(),))
+ log.debug('User: %s, ACTIVEDIRECTORY: Search Exception:\n%s' % (username, traceback.format_exc(),))
return (failuremode, '')
# end search
@@ -84,11 +87,11 @@
l.simple_bind_s(_getsubs(options, 'bind-user', vars), _getsubs(options, 'bind-password', vars))
except Exception:
if debug:
- print('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc()))
+ log.debug('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc()))
return (failuremode, '')
if debug:
- print "User: %s, ACTIVEDIRECTORY: True" % (username)
+ log.debug("User: %s, ACTIVEDIRECTORY: True" % (username))
return (True, _getsubs(options, 'auto-register-username', vars))
def authenticateUser(self, user, password, options, debug=False):
diff -r 03e964afd1578a1df236e70cbe55659967458028 -r 77ad730cd6866e89cb8bcad865cacef66a15fd49 lib/galaxy/auth/providers/alwaysreject.py
--- a/lib/galaxy/auth/providers/alwaysreject.py
+++ b/lib/galaxy/auth/providers/alwaysreject.py
@@ -6,6 +6,9 @@
from ..providers import AuthProvider
+import logging
+log = logging.getLogger(__name__)
+
class AlwaysReject(AuthProvider):
"""A simple authenticator that just accepts users (does not care about their
@@ -24,7 +27,7 @@
See abstract method documentation.
"""
if debug:
- print ("User: %s, ALWAYSREJECT: None" % (user.email))
+ log.debug("User: %s, ALWAYSREJECT: None" % (user.email))
return None
diff -r 03e964afd1578a1df236e70cbe55659967458028 -r 77ad730cd6866e89cb8bcad865cacef66a15fd49 lib/galaxy/auth/providers/localdb.py
--- a/lib/galaxy/auth/providers/localdb.py
+++ b/lib/galaxy/auth/providers/localdb.py
@@ -25,7 +25,7 @@
"""
user_ok = user.check_password(password)
if debug:
- print ("User: %s, LOCALDB: %s" % (user.email, user_ok))
+ log.debug("User: %s, LOCALDB: %s" % (user.email, user_ok))
return user_ok
https://bitbucket.org/galaxy/galaxy-central/commits/bf6d42e86784/
Changeset: bf6d42e86784
User: jmchilton
Date: 2015-03-02 03:12:38+00:00
Summary: PEP-8 method names in galaxy.auth and submodules.
Affected #: 5 files
diff -r 77ad730cd6866e89cb8bcad865cacef66a15fd49 -r bf6d42e8678467f7f369bc22d5ddb4abe7a915c7 lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -62,14 +62,14 @@
plugin = self.__plugins_dict.get(typeelem.text)()
# check filterelem
- filter_elem = _getChildElement(authelem, 'filter')
+ filter_elem = _get_child_element(authelem, 'filter')
if filter_elem is not None:
filter_template = str(filter_elem.text)
else:
filter_template = None
# extract options
- optionselem = _getChildElement(authelem, 'options')
+ optionselem = _get_child_element(authelem, 'options')
options = {}
if optionselem is not None:
for opt in optionselem:
@@ -86,8 +86,8 @@
"""Checks if the provided email is allowed to register."""
message = ''
status = 'done'
- for provider, options in self.activeAuthProviderGenerator(email, password):
- allowreg = _getTriState(options, 'allow-register', True)
+ for provider, options in self.active_authenticators(email, password):
+ allowreg = _get_tri_state(options, 'allow-register', True)
if allowreg is None: # i.e. challenge
authresult, msg = provider.authenticate(email, password, options)
if authresult is True:
@@ -109,7 +109,7 @@
Checks the email/password using auth providers in order. If a match is
found, returns the 'auto-register' option for that provider.
"""
- for provider, options in self.activeAuthProviderGenerator(email, password, debug):
+ for provider, options in self.active_authenticators(email, password, debug):
if provider is None:
if debug:
log.debug( "Unable to find module: %s" % options )
@@ -129,7 +129,7 @@
break # end for loop if we can't make a unique username
if debug:
log.debug( "Email: %s, auto-register with username: %s" % (email, autousername) )
- return (_getBool(options, 'auto-register', False), autousername)
+ return (_get_bool(options, 'auto-register', False), autousername)
elif authresult is None:
log.debug( "Email: %s, stopping due to failed non-continue" % (email) )
break # end authentication (skip rest)
@@ -137,12 +137,12 @@
def check_password(self, user, password):
"""Checks the email/password using auth providers."""
- for provider, options in self.activeAuthProviderGenerator(user.email, password):
+ for provider, options in self.active_authenticators(user.email, password):
if provider is None:
if self.debug:
log.debug( "Unable to find module: %s" % options )
else:
- authresult = provider.authenticateUser(user, password, options)
+ authresult = provider.authenticate_user(user, password, options)
if authresult is True:
return True # accept user
elif authresult is None:
@@ -153,13 +153,13 @@
"""Checks that auth provider allows password changes and current_password
matches.
"""
- for provider, options in self.activeAuthProviderGenerator(user.email, current_password):
+ for provider, options in self.active_authenticators(user.email, current_password):
if provider is None:
if self.debug:
log.debug( "Unable to find module: %s" % options )
else:
- if _getBool(options, "allow-password-change", False):
- authresult = provider.authenticateUser(user, current_password, options)
+ if _get_bool(options, "allow-password-change", False):
+ authresult = provider.authenticate_user(user, current_password, options)
if authresult is True:
return (True, '') # accept user
elif authresult is None:
@@ -168,7 +168,7 @@
return (False, 'Password change not supported')
return (False, 'Invalid current password')
- def activeAuthProviderGenerator(self, username, password):
+ def active_authenticators(self, username, password):
"""Yields AuthProvider instances for the provided configfile that match the
filters.
"""
@@ -189,21 +189,21 @@
Authenticator = namedtuple('Authenticator', ['plugin', 'filter_template', 'options'])
-def _getBool(d, k, o):
+def _get_bool(d, k, o):
if k in d:
return string_as_bool(d[k])
else:
return o
-def _getTriState(d, k, o):
+def _get_tri_state(d, k, o):
if k in d:
return string_as_bool_or_none(d[k])
else:
return o
-def _getChildElement(parent, childname):
+def _get_child_element(parent, childname):
try:
return parent.iter(childname).next()
except StopIteration:
diff -r 77ad730cd6866e89cb8bcad865cacef66a15fd49 -r bf6d42e8678467f7f369bc22d5ddb4abe7a915c7 lib/galaxy/auth/providers/__init__.py
--- a/lib/galaxy/auth/providers/__init__.py
+++ b/lib/galaxy/auth/providers/__init__.py
@@ -38,7 +38,7 @@
"""
@abc.abstractmethod
- def authenticateUser(self, user, password, options, debug=False):
+ def authenticate_user(self, user, password, options, debug=False):
"""
Same as authenticate() method, except an User object is provided instead
of a username.
diff -r 77ad730cd6866e89cb8bcad865cacef66a15fd49 -r bf6d42e8678467f7f369bc22d5ddb4abe7a915c7 lib/galaxy/auth/providers/activedirectory.py
--- a/lib/galaxy/auth/providers/activedirectory.py
+++ b/lib/galaxy/auth/providers/activedirectory.py
@@ -11,7 +11,7 @@
log = logging.getLogger(__name__)
-def _getsubs(d, k, vars, default=''):
+def _get_subs(d, k, vars, default=''):
if k in d:
return str(d[k]).format(**vars)
return str(default).format(**vars)
@@ -52,14 +52,14 @@
try:
# setup connection
ldap.set_option(ldap.OPT_REFERRALS, 0)
- l = ldap.initialize(_getsubs(options, 'server', vars))
+ l = ldap.initialize(_get_subs(options, 'server', vars))
l.protocol_version = 3
- l.simple_bind_s(_getsubs(options, 'search-user', vars), _getsubs(options, 'search-password', vars))
+ l.simple_bind_s(_get_subs(options, 'search-user', vars), _get_subs(options, 'search-password', vars))
scope = ldap.SCOPE_SUBTREE
# setup search
attributes = map(lambda s: s.strip().format(**vars), options['search-fields'].split(','))
- result = l.search(_getsubs(options, 'search-base', vars), scope, _getsubs(options, 'search-filter', vars), attributes)
+ result = l.search(_get_subs(options, 'search-base', vars), scope, _get_subs(options, 'search-filter', vars), attributes)
# parse results
_, suser = l.result(result, 60)
@@ -82,9 +82,9 @@
try:
# setup connection
ldap.set_option(ldap.OPT_REFERRALS, 0)
- l = ldap.initialize(_getsubs(options, 'server', vars))
+ l = ldap.initialize(_get_subs(options, 'server', vars))
l.protocol_version = 3
- l.simple_bind_s(_getsubs(options, 'bind-user', vars), _getsubs(options, 'bind-password', vars))
+ l.simple_bind_s(_get_subs(options, 'bind-user', vars), _get_subs(options, 'bind-password', vars))
except Exception:
if debug:
log.debug('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc()))
@@ -92,9 +92,9 @@
if debug:
log.debug("User: %s, ACTIVEDIRECTORY: True" % (username))
- return (True, _getsubs(options, 'auto-register-username', vars))
+ return (True, _get_subs(options, 'auto-register-username', vars))
- def authenticateUser(self, user, password, options, debug=False):
+ def authenticate_user(self, user, password, options, debug=False):
"""
See abstract method documentation.
"""
diff -r 77ad730cd6866e89cb8bcad865cacef66a15fd49 -r bf6d42e8678467f7f369bc22d5ddb4abe7a915c7 lib/galaxy/auth/providers/alwaysreject.py
--- a/lib/galaxy/auth/providers/alwaysreject.py
+++ b/lib/galaxy/auth/providers/alwaysreject.py
@@ -22,7 +22,7 @@
"""
return (None, '')
- def authenticateUser(self, user, password, options, debug=False):
+ def authenticate_user(self, user, password, options, debug=False):
"""
See abstract method documentation.
"""
diff -r 77ad730cd6866e89cb8bcad865cacef66a15fd49 -r bf6d42e8678467f7f369bc22d5ddb4abe7a915c7 lib/galaxy/auth/providers/localdb.py
--- a/lib/galaxy/auth/providers/localdb.py
+++ b/lib/galaxy/auth/providers/localdb.py
@@ -19,7 +19,7 @@
"""
return (False, '') # it can never auto-create based of localdb (chicken-egg)
- def authenticateUser(self, user, password, options, debug=False):
+ def authenticate_user(self, user, password, options, debug=False):
"""
See abstract method documentation.
"""
https://bitbucket.org/galaxy/galaxy-central/commits/c70db1a9c9a9/
Changeset: c70db1a9c9a9
User: jmchilton
Date: 2015-03-02 03:15:26+00:00
Summary: PEP-8 variable names in galaxy.auth and submodules.
Affected #: 2 files
diff -r bf6d42e8678467f7f369bc22d5ddb4abe7a915c7 -r c70db1a9c9a9ad6915d8e282e371d27cf9cb84e9 lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -53,26 +53,26 @@
def __init_authenticators(self, auth_config_file):
# parse XML
ct = xml.etree.ElementTree.parse(auth_config_file)
- confroot = ct.getroot()
+ conf_root = ct.getroot()
authenticators = []
# process authenticators
- for authelem in confroot.getchildren():
- typeelem = authelem.iter('type').next()
- plugin = self.__plugins_dict.get(typeelem.text)()
+ for auth_elem in conf_root.getchildren():
+ type_elem = auth_elem.iter('type').next()
+ plugin = self.__plugins_dict.get(type_elem.text)()
# check filterelem
- filter_elem = _get_child_element(authelem, 'filter')
+ filter_elem = _get_child_element(auth_elem, 'filter')
if filter_elem is not None:
filter_template = str(filter_elem.text)
else:
filter_template = None
# extract options
- optionselem = _get_child_element(authelem, 'options')
+ options_elem = _get_child_element(auth_elem, 'options')
options = {}
- if optionselem is not None:
- for opt in optionselem:
+ if options_elem is not None:
+ for opt in options_elem:
options[opt.tag] = opt.text
authenticator = Authenticator(
plugin=plugin,
@@ -87,18 +87,18 @@
message = ''
status = 'done'
for provider, options in self.active_authenticators(email, password):
- allowreg = _get_tri_state(options, 'allow-register', True)
- if allowreg is None: # i.e. challenge
- authresult, msg = provider.authenticate(email, password, options)
- if authresult is True:
+ allow_reg = _get_tri_state(options, 'allow-register', True)
+ if allow_reg is None: # i.e. challenge
+ auth_result, msg = provider.authenticate(email, password, options)
+ if auth_result is True:
break
- if authresult is None:
+ if auth_result is None:
message = 'Invalid email address or password'
status = 'error'
break
- elif allowreg is True:
+ elif allow_reg is True:
break
- elif allowreg is False:
+ elif allow_reg is False:
message = 'Account registration not required for your account. Please simply login.'
status = 'error'
break
@@ -114,23 +114,23 @@
if debug:
log.debug( "Unable to find module: %s" % options )
else:
- authresult, autousername = provider.authenticate(email, password, options, debug)
- autousername = str(autousername).lower()
- if authresult is True:
+ auth_result, auto_username = provider.authenticate(email, password, options, debug)
+ auto_username = str(auto_username).lower()
+ if auth_result is True:
# make username unique
- if validate_publicname( trans, autousername ) != '':
+ if validate_publicname( trans, auto_username ) != '':
i = 1
while i <= 10: # stop after 10 tries
- if validate_publicname( trans, "%s-%i" % (autousername, i) ) == '':
- autousername = "%s-%i" % (autousername, i)
+ if validate_publicname( trans, "%s-%i" % (auto_username, i) ) == '':
+ auto_username = "%s-%i" % (auto_username, i)
break
i += 1
else:
break # end for loop if we can't make a unique username
if debug:
- log.debug( "Email: %s, auto-register with username: %s" % (email, autousername) )
- return (_get_bool(options, 'auto-register', False), autousername)
- elif authresult is None:
+ log.debug( "Email: %s, auto-register with username: %s" % (email, auto_username) )
+ return (_get_bool(options, 'auto-register', False), auto_username)
+ elif auth_result is None:
log.debug( "Email: %s, stopping due to failed non-continue" % (email) )
break # end authentication (skip rest)
return (False, '')
@@ -142,10 +142,10 @@
if self.debug:
log.debug( "Unable to find module: %s" % options )
else:
- authresult = provider.authenticate_user(user, password, options)
- if authresult is True:
+ auth_result = provider.authenticate_user(user, password, options)
+ if auth_result is True:
return True # accept user
- elif authresult is None:
+ elif auth_result is None:
break # end authentication (skip rest)
return False
@@ -159,10 +159,10 @@
log.debug( "Unable to find module: %s" % options )
else:
if _get_bool(options, "allow-password-change", False):
- authresult = provider.authenticate_user(user, current_password, options)
- if authresult is True:
+ auth_result = provider.authenticate_user(user, current_password, options)
+ if auth_result is True:
return (True, '') # accept user
- elif authresult is None:
+ elif auth_result is None:
break # end authentication (skip rest)
else:
return (False, 'Password change not supported')
diff -r bf6d42e8678467f7f369bc22d5ddb4abe7a915c7 -r c70db1a9c9a9ad6915d8e282e371d27cf9cb84e9 lib/galaxy/auth/providers/activedirectory.py
--- a/lib/galaxy/auth/providers/activedirectory.py
+++ b/lib/galaxy/auth/providers/activedirectory.py
@@ -35,16 +35,16 @@
log.debug("Username: %s" % username)
log.debug("Options: %s" % options)
- failuremode = False # reject but continue
+ failure_mode = False # reject but continue
if options.get('continue-on-failure', 'False') == 'False':
- failuremode = None # reject and do not continue
+ failure_mode = None # reject and do not continue
try:
import ldap
except:
if debug:
log.debug("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
- return (failuremode, '')
+ return (failure_mode, '')
# do AD search (if required)
vars = {'username': username, 'password': password}
@@ -75,7 +75,7 @@
except Exception:
if debug:
log.debug('User: %s, ACTIVEDIRECTORY: Search Exception:\n%s' % (username, traceback.format_exc(),))
- return (failuremode, '')
+ return (failure_mode, '')
# end search
# bind as user to check their credentials
@@ -88,7 +88,7 @@
except Exception:
if debug:
log.debug('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc()))
- return (failuremode, '')
+ return (failure_mode, '')
if debug:
log.debug("User: %s, ACTIVEDIRECTORY: True" % (username))
https://bitbucket.org/galaxy/galaxy-central/commits/3a144d3b729d/
Changeset: 3a144d3b729d
User: dannon
Date: 2015-03-02 15:12:21+00:00
Summary: Fix customauth to be python2.6 compatible.
Affected #: 1 file
diff -r c70db1a9c9a9ad6915d8e282e371d27cf9cb84e9 -r 3a144d3b729d27f35905bdf278e536d48ffc3c0b lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -58,7 +58,7 @@
authenticators = []
# process authenticators
for auth_elem in conf_root.getchildren():
- type_elem = auth_elem.iter('type').next()
+ type_elem = auth_elem.find('type')
plugin = self.__plugins_dict.get(type_elem.text)()
# check filterelem
@@ -204,7 +204,4 @@
def _get_child_element(parent, childname):
- try:
- return parent.iter(childname).next()
- except StopIteration:
- return None
+ return parent.find(childname)
https://bitbucket.org/galaxy/galaxy-central/commits/729c25276e7d/
Changeset: 729c25276e7d
User: dannon
Date: 2015-03-02 15:15:27+00:00
Summary: Remove unnecessary complexity of _get_child_element
Affected #: 1 file
diff -r 3a144d3b729d27f35905bdf278e536d48ffc3c0b -r 729c25276e7da9c28eff9d678c819bfb40a13d2c lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -62,14 +62,14 @@
plugin = self.__plugins_dict.get(type_elem.text)()
# check filterelem
- filter_elem = _get_child_element(auth_elem, 'filter')
+ filter_elem = auth_elem.find('filter')
if filter_elem is not None:
filter_template = str(filter_elem.text)
else:
filter_template = None
# extract options
- options_elem = _get_child_element(auth_elem, 'options')
+ options_elem = auth_elem.find('options')
options = {}
if options_elem is not None:
for opt in options_elem:
@@ -201,7 +201,3 @@
return string_as_bool_or_none(d[k])
else:
return o
-
-
-def _get_child_element(parent, childname):
- return parent.find(childname)
https://bitbucket.org/galaxy/galaxy-central/commits/0a878e33a786/
Changeset: 0a878e33a786
User: carlfeberhard
Date: 2015-03-02 16:20:37+00:00
Summary: Fix to sessionStorage Model to surpress QUOTA DOMExceptions when Safari users are in private browsing mode
Affected #: 3 files
diff -r 729c25276e7da9c28eff9d678c819bfb40a13d2c -r 0a878e33a78666e7c36dd447a017307cb113a462 client/galaxy/scripts/mvc/base-mvc.js
--- a/client/galaxy/scripts/mvc/base-mvc.js
+++ b/client/galaxy/scripts/mvc/base-mvc.js
@@ -94,7 +94,7 @@
if( !options.silent ){
model.trigger( 'request', model, {}, options );
}
- var returned;
+ var returned = {};
switch( method ){
case 'create' : returned = this._create( model ); break;
case 'read' : returned = this._read( model ); break;
@@ -111,9 +111,19 @@
/** set storage to the stringified item */
_create : function( model ){
- var json = model.toJSON(),
- set = sessionStorage.setItem( model.id, JSON.stringify( json ) );
- return ( set === null )?( set ):( json );
+ try {
+ var json = model.toJSON(),
+ set = sessionStorage.setItem( model.id, JSON.stringify( json ) );
+ return ( set === null )?( set ):( json );
+ // DOMException is thrown in Safari if in private browsing mode and sessionStorage is attempted:
+ // http://stackoverflow.com/questions/14555347
+ // TODO: this could probably use a more general soln - like detecting priv. mode + safari => non-ajaxing Model
+ } catch( err ){
+ if( !( ( err instanceof DOMException ) && ( navigator.userAgent.indexOf("Safari") > -1 ) ) ){
+ throw err;
+ }
+ }
+ return null;
},
/** read and parse json from storage */
diff -r 729c25276e7da9c28eff9d678c819bfb40a13d2c -r 0a878e33a78666e7c36dd447a017307cb113a462 static/scripts/mvc/base-mvc.js
--- a/static/scripts/mvc/base-mvc.js
+++ b/static/scripts/mvc/base-mvc.js
@@ -94,7 +94,7 @@
if( !options.silent ){
model.trigger( 'request', model, {}, options );
}
- var returned;
+ var returned = {};
switch( method ){
case 'create' : returned = this._create( model ); break;
case 'read' : returned = this._read( model ); break;
@@ -111,9 +111,19 @@
/** set storage to the stringified item */
_create : function( model ){
- var json = model.toJSON(),
- set = sessionStorage.setItem( model.id, JSON.stringify( json ) );
- return ( set === null )?( set ):( json );
+ try {
+ var json = model.toJSON(),
+ set = sessionStorage.setItem( model.id, JSON.stringify( json ) );
+ return ( set === null )?( set ):( json );
+ // DOMException is thrown in Safari if in private browsing mode and sessionStorage is attempted:
+ // http://stackoverflow.com/questions/14555347
+ // TODO: this could probably use a more general soln - like detecting priv. mode + safari => non-ajaxing Model
+ } catch( err ){
+ if( !( ( err instanceof DOMException ) && ( navigator.userAgent.indexOf("Safari") > -1 ) ) ){
+ throw err;
+ }
+ }
+ return null;
},
/** read and parse json from storage */
diff -r 729c25276e7da9c28eff9d678c819bfb40a13d2c -r 0a878e33a78666e7c36dd447a017307cb113a462 static/scripts/packed/mvc/base-mvc.js
--- a/static/scripts/packed/mvc/base-mvc.js
+++ b/static/scripts/packed/mvc/base-mvc.js
@@ -1,1 +1,1 @@
-define(["utils/add-logging","utils/localization"],function(h,b){var i={logger:null,_logNamespace:"?",log:function(){if(this.logger){var k=this.logger.log;if(typeof this.logger.log==="object"){k=Function.prototype.bind.call(this.logger.log,this.logger)}return k.apply(this.logger,arguments)}return undefined}};h(i);var a=Backbone.Model.extend({initialize:function(l){this._checkEnabledSessionStorage();if(!l.id){throw new Error("SessionStorageModel requires an id in the initial attributes")}this.id=l.id;var k=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,k,l),{silent:true});this.on("change",function(){this.save()})},_checkEnabledSessionStorage:function(){try{return sessionStorage.length}catch(k){alert("Please enable cookies in your browser for this Galaxy site");return false}},sync:function(n,l,k){if(!k.silent){l.trigger("request",l,{},k)}var m;switch(n){case"create":m=this._create(l);break;case"read":m=this._read(l);break;case"update":m=this._update(l);break;case"delete":m=this._delete(l);break}if(m!==undefined||m!==null){if(k.success){k.success()}}else{if(k.error){k.error()}}return m},_create:function(k){var l=k.toJSON(),m=sessionStorage.setItem(k.id,JSON.stringify(l));return(m===null)?(m):(l)},_read:function(k){return JSON.parse(sessionStorage.getItem(k.id))},_update:function(k){return k._create(k)},_delete:function(k){return sessionStorage.removeItem(k.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){a.prototype=_.omit(a.prototype,"url","urlRoot")}());function j(n,m){var k=Array.prototype.slice.call(arguments,0),l=k.pop();k.unshift(l);return _.defaults.apply(_,k)}var g={searchAttributes:[],searchAliases:{},searchAttribute:function(m,k){var l=this.get(m);if(!k||(l===undefined||l===null)){return false}if(_.isArray(l)){return this._searchArrayAttribute(l,k)}return(l.toString().toLowerCase().indexOf(k.toLowerCase())!==-1)},_searchArrayAttribute:function(l,k){k=k.toLowerCase();return _.any(l,function(m){return(m.toString().toLowerCase().indexOf(k.toLowerCase())!==-1)})},search:function(k){var l=this;return _.filter(this.searchAttributes,function(m){return l.searchAttribute(m,k)})},matches:function(l){var n="=",k=l.split(n);if(k.length>=2){var m=k[0];m=this.searchAliases[m]||m;return this.searchAttribute(m,k[1])}return !!this.search(l).length},matchesAll:function(l){var k=this;l=l.match(/(".*"|\w*=".*"|\S*)/g).filter(function(m){return !!m});return _.all(l,function(m){m=m.replace(/"/g,"");return k.matches(m)})}};var c={hiddenUntilActivated:function(k,m){m=m||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,m||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");this.hidden=this.isHidden();if(k){var l=this;k.on("click",function(n){l.toggle(l.HUAVOptions.showSpeed)})}},isHidden:function(){return(this.HUAVOptions.$elementShown.is(":hidden"))},toggle:function(){if(this.hidden){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this);this.trigger("hiddenUntilActivated:shown",this)}this.hidden=false}else{if(_.isFunction(this.HUAVOptions.onhide)){this.HUAVOptions.onhide.call(this);this.trigger("hiddenUntilActivated:hidden",this)}this.hidden=true}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}};var f={initialize:function(k){this.draggable=k.draggable||false},$dragHandle:function(){return this.$(".title-bar")},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var k=this.$dragHandle().attr("draggable",true).get(0);k.addEventListener("dragstart",this.dragStartHandler,false);k.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var k=this.$dragHandle().attr("draggable",false).get(0);k.removeEventListener("dragstart",this.dragStartHandler,false);k.removeEventListener("dragend",this.dragEndHandler,false)},_dragStartHandler:function(k){k.dataTransfer.effectAllowed="move";k.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));this.trigger("draggable:dragstart",k,this);return false},_dragEndHandler:function(k){this.trigger("draggable:dragend",k,this);return false}};var d={initialize:function(k){this.selectable=k.selectable||false;this.selected=k.selected||false},$selector:function(){return this.$(".selector")},_renderSelected:function(){this.$selector().find("span").toggleClass("fa-check-square-o",this.selected).toggleClass("fa-square-o",!this.selected)},toggleSelector:function(){if(!this.$selector().is(":visible")){this.showSelector()}else{this.hideSelector()}},showSelector:function(k){k=k!==undefined?k:this.fxSpeed;this.selectable=true;this.trigger("selectable",true,this);this._renderSelected();this.$selector().show(k)},hideSelector:function(k){k=k!==undefined?k:this.fxSpeed;this.selectable=false;this.trigger("selectable",false,this);this.$selector().hide(k)},toggleSelect:function(k){if(this.selected){this.deselect(k)}else{this.select(k)}},select:function(k){if(!this.selected){this.trigger("selected",this,k);this.selected=true;this._renderSelected()}return false},deselect:function(k){if(this.selected){this.trigger("de-selected",this,k);this.selected=false;this._renderSelected()}return false}};function e(l,k){k=k||"model";var m=_.template(l.join(""));return function(o,n){var p={view:n||{},_l:b};p[k]=o||{};return m(p)}}return{LoggableMixin:i,SessionStorageModel:a,mixin:j,SearchableModelMixin:g,HiddenUntilActivatedViewMixin:c,DraggableViewMixin:f,SelectableViewMixin:d,wrapTemplate:e}});
\ No newline at end of file
+define(["utils/add-logging","utils/localization"],function(h,b){var i={logger:null,_logNamespace:"?",log:function(){if(this.logger){var k=this.logger.log;if(typeof this.logger.log==="object"){k=Function.prototype.bind.call(this.logger.log,this.logger)}return k.apply(this.logger,arguments)}return undefined}};h(i);var a=Backbone.Model.extend({initialize:function(l){this._checkEnabledSessionStorage();if(!l.id){throw new Error("SessionStorageModel requires an id in the initial attributes")}this.id=l.id;var k=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,k,l),{silent:true});this.on("change",function(){this.save()})},_checkEnabledSessionStorage:function(){try{return sessionStorage.length}catch(k){alert("Please enable cookies in your browser for this Galaxy site");return false}},sync:function(n,l,k){if(!k.silent){l.trigger("request",l,{},k)}var m={};switch(n){case"create":m=this._create(l);break;case"read":m=this._read(l);break;case"update":m=this._update(l);break;case"delete":m=this._delete(l);break}if(m!==undefined||m!==null){if(k.success){k.success()}}else{if(k.error){k.error()}}return m},_create:function(k){try{var l=k.toJSON(),n=sessionStorage.setItem(k.id,JSON.stringify(l));return(n===null)?(n):(l)}catch(m){if(!((m instanceof DOMException)&&(navigator.userAgent.indexOf("Safari")>-1))){throw m}}return null},_read:function(k){return JSON.parse(sessionStorage.getItem(k.id))},_update:function(k){return k._create(k)},_delete:function(k){return sessionStorage.removeItem(k.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){a.prototype=_.omit(a.prototype,"url","urlRoot")}());function j(n,m){var k=Array.prototype.slice.call(arguments,0),l=k.pop();k.unshift(l);return _.defaults.apply(_,k)}var g={searchAttributes:[],searchAliases:{},searchAttribute:function(m,k){var l=this.get(m);if(!k||(l===undefined||l===null)){return false}if(_.isArray(l)){return this._searchArrayAttribute(l,k)}return(l.toString().toLowerCase().indexOf(k.toLowerCase())!==-1)},_searchArrayAttribute:function(l,k){k=k.toLowerCase();return _.any(l,function(m){return(m.toString().toLowerCase().indexOf(k.toLowerCase())!==-1)})},search:function(k){var l=this;return _.filter(this.searchAttributes,function(m){return l.searchAttribute(m,k)})},matches:function(l){var n="=",k=l.split(n);if(k.length>=2){var m=k[0];m=this.searchAliases[m]||m;return this.searchAttribute(m,k[1])}return !!this.search(l).length},matchesAll:function(l){var k=this;l=l.match(/(".*"|\w*=".*"|\S*)/g).filter(function(m){return !!m});return _.all(l,function(m){m=m.replace(/"/g,"");return k.matches(m)})}};var c={hiddenUntilActivated:function(k,m){m=m||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,m||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");this.hidden=this.isHidden();if(k){var l=this;k.on("click",function(n){l.toggle(l.HUAVOptions.showSpeed)})}},isHidden:function(){return(this.HUAVOptions.$elementShown.is(":hidden"))},toggle:function(){if(this.hidden){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this);this.trigger("hiddenUntilActivated:shown",this)}this.hidden=false}else{if(_.isFunction(this.HUAVOptions.onhide)){this.HUAVOptions.onhide.call(this);this.trigger("hiddenUntilActivated:hidden",this)}this.hidden=true}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}};var f={initialize:function(k){this.draggable=k.draggable||false},$dragHandle:function(){return this.$(".title-bar")},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var k=this.$dragHandle().attr("draggable",true).get(0);k.addEventListener("dragstart",this.dragStartHandler,false);k.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var k=this.$dragHandle().attr("draggable",false).get(0);k.removeEventListener("dragstart",this.dragStartHandler,false);k.removeEventListener("dragend",this.dragEndHandler,false)},_dragStartHandler:function(k){k.dataTransfer.effectAllowed="move";k.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));this.trigger("draggable:dragstart",k,this);return false},_dragEndHandler:function(k){this.trigger("draggable:dragend",k,this);return false}};var d={initialize:function(k){this.selectable=k.selectable||false;this.selected=k.selected||false},$selector:function(){return this.$(".selector")},_renderSelected:function(){this.$selector().find("span").toggleClass("fa-check-square-o",this.selected).toggleClass("fa-square-o",!this.selected)},toggleSelector:function(){if(!this.$selector().is(":visible")){this.showSelector()}else{this.hideSelector()}},showSelector:function(k){k=k!==undefined?k:this.fxSpeed;this.selectable=true;this.trigger("selectable",true,this);this._renderSelected();this.$selector().show(k)},hideSelector:function(k){k=k!==undefined?k:this.fxSpeed;this.selectable=false;this.trigger("selectable",false,this);this.$selector().hide(k)},toggleSelect:function(k){if(this.selected){this.deselect(k)}else{this.select(k)}},select:function(k){if(!this.selected){this.trigger("selected",this,k);this.selected=true;this._renderSelected()}return false},deselect:function(k){if(this.selected){this.trigger("de-selected",this,k);this.selected=false;this._renderSelected()}return false}};function e(l,k){k=k||"model";var m=_.template(l.join(""));return function(o,n){var p={view:n||{},_l:b};p[k]=o||{};return m(p)}}return{LoggableMixin:i,SessionStorageModel:a,mixin:j,SearchableModelMixin:g,HiddenUntilActivatedViewMixin:c,DraggableViewMixin:f,SelectableViewMixin:d,wrapTemplate:e}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/8612b5dfa37e/
Changeset: 8612b5dfa37e
User: dan
Date: 2015-03-02 16:34:55+00:00
Summary: Add a 10 second timeout to loading data URLs for Tool Data Tables.
Affected #: 1 file
diff -r 0a878e33a78666e7c36dd447a017307cb113a462 -r 8612b5dfa37e72b2cf093a0a517e6f1110b8372a lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -263,7 +263,7 @@
self.data = []
self.configure_and_load( config_element, tool_data_path, from_shed_config)
- def configure_and_load( self, config_element, tool_data_path, from_shed_config=False):
+ def configure_and_load( self, config_element, tool_data_path, from_shed_config=False, url_timeout=10 ):
"""
Configure and load table from an XML element.
"""
@@ -289,7 +289,7 @@
if filename:
tmp_file = NamedTemporaryFile( prefix='TTDT_URL_%s-' % self.name )
try:
- tmp_file.write( urlopen( filename ).read() )
+ tmp_file.write( urlopen( filename, timeout=url_timeout ).read() )
except Exception, e:
log.error( 'Error loading Data Table URL "%s": %s', filename, e )
continue
https://bitbucket.org/galaxy/galaxy-central/commits/4d2345e34c27/
Changeset: 4d2345e34c27
User: dannon
Date: 2015-03-02 17:29:54+00:00
Summary: Fix for auth when user doesn't exist.
Affected #: 1 file
diff -r 8612b5dfa37e72b2cf093a0a517e6f1110b8372a -r 4d2345e34c27fa86812fb5b892bed1cf51e12ef6 lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -109,7 +109,7 @@
Checks the email/password using auth providers in order. If a match is
found, returns the 'auto-register' option for that provider.
"""
- for provider, options in self.active_authenticators(email, password, debug):
+ for provider, options in self.active_authenticators(email, password):
if provider is None:
if debug:
log.debug( "Unable to find module: %s" % options )
https://bitbucket.org/galaxy/galaxy-central/commits/e34af1e6e532/
Changeset: e34af1e6e532
User: jmchilton
Date: 2015-03-02 18:45:12+00:00
Summary: Update basic.py to allow collection reduction with new tool form.
Affected #: 1 file
diff -r 4d2345e34c27fa86812fb5b892bed1cf51e12ef6 -r e34af1e6e532099d7b3a6f67f8c22502c7d2a189 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1992,10 +1992,19 @@
value = [ int( value_part ) for value_part in value.split( "," ) ]
if isinstance( value, list ):
rval = []
+ found_hdca = False
for single_value in value:
- if isinstance( single_value, dict ):
- assert single_value['src'] == 'hda'
- rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id( single_value[ 'id' ] ) ) )
+ if found_hdca:
+ raise ValueError("Only one collection may be supplied to parameter.")
+ if isinstance( single_value, dict ) and 'src' in single_value and 'id' in single_value:
+ if single_value['src'] == 'hda':
+ rval.append(trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(single_value['id']) ))
+ elif single_value['src'] == 'hdca':
+ found_hdca = True
+ decoded_id = trans.app.security.decode_id( single_value[ 'id' ] )
+ rval = trans.sa_session.query( trans.app.model.HistoryDatasetCollectionAssociation ).get( decoded_id )
+ else:
+ raise ValueError("Unknown input source %s passed to job submission API." % single_value['src'])
else:
rval.append( trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( single_value ) )
elif isinstance( value, trans.app.model.HistoryDatasetAssociation ):
https://bitbucket.org/galaxy/galaxy-central/commits/1e8f541217da/
Changeset: 1e8f541217da
User: carlfeberhard
Date: 2015-03-02 19:22:00+00:00
Summary: Fix to remove validation of genome builds since some data source tools will assign invalid genome builds and later validation makes these hdas un-updatable
Affected #: 1 file
diff -r e34af1e6e532099d7b3a6f67f8c22502c7d2a189 -r 1e8f541217daf3ddf77a648c912129c7247cc96e lib/galaxy/managers/base.py
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -789,10 +789,13 @@
# TODO: is this correct?
if val is None:
return '?'
- for genome_build_shortname, longname in self.app.genome_builds.get_genome_build_names( trans=trans ):
- if val == genome_build_shortname:
- return val
- raise exceptions.RequestParameterInvalidException( "invalid reference", key=key, val=val )
+ # currently, data source sites like UCSC are able to set the genome build to non-local build names
+ # afterwards, attempting to validate the whole model will choke here
+ # for genome_build_shortname, longname in self.app.genome_builds.get_genome_build_names( trans=trans ):
+ # if val == genome_build_shortname:
+ # return val
+ # raise exceptions.RequestParameterInvalidException( "invalid reference", key=key, val=val )
+ return val
# def slug( self, trans, item, key, val ):
# """validate slug"""
https://bitbucket.org/galaxy/galaxy-central/commits/2a92468416e8/
Changeset: 2a92468416e8
User: dannon
Date: 2015-03-02 19:54:29+00:00
Summary: Rearranging the layers of middleware to allow sentry and debug to coexist without exploding (but you probably don't want to use both at once anyway)
Affected #: 1 file
diff -r 1e8f541217daf3ddf77a648c912129c7247cc96e -r 2a92468416e81c70a15ecb3d3491fbbfa2679b64 lib/galaxy/webapps/tool_shed/buildapp.py
--- a/lib/galaxy/webapps/tool_shed/buildapp.py
+++ b/lib/galaxy/webapps/tool_shed/buildapp.py
@@ -176,14 +176,6 @@
from paste import recursive
app = recursive.RecursiveMiddleware( app, conf )
log.debug( "Enabling 'recursive' middleware" )
- # If sentry logging is enabled, log here before propogating up to
- # the error middleware
- # TODO sentry config is duplicated between tool_shed/galaxy, refactor this.
- sentry_dsn = conf.get( 'sentry_dsn', None )
- if sentry_dsn:
- from galaxy.web.framework.middleware.sentry import Sentry
- log.debug( "Enabling 'sentry' middleware" )
- app = Sentry( app, sentry_dsn )
# Various debug middleware that can only be turned on if the debug
# flag is set, either because they are insecure or greatly hurt
# performance
@@ -223,6 +215,14 @@
from paste.translogger import TransLogger
app = TransLogger( app )
log.debug( "Enabling 'trans logger' middleware" )
+ # If sentry logging is enabled, log here before propogating up to
+ # the error middleware
+ # TODO sentry config is duplicated between tool_shed/galaxy, refactor this.
+ sentry_dsn = conf.get( 'sentry_dsn', None )
+ if sentry_dsn:
+ from galaxy.web.framework.middleware.sentry import Sentry
+ log.debug( "Enabling 'sentry' middleware" )
+ app = Sentry( app, sentry_dsn )
# X-Forwarded-Host handling
from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
app = XForwardedHostMiddleware( app )
https://bitbucket.org/galaxy/galaxy-central/commits/e9dcf9066aaa/
Changeset: e9dcf9066aaa
User: natefoo
Date: 2015-03-02 19:56:01+00:00
Summary: Make the UCSC Browser to pull new builds from (in the cron script) a
command line argument. Default is UCSC Main, but for Galaxy Test and
Main we use UCSC Test.
Affected #: 1 file
diff -r 2a92468416e81c70a15ecb3d3491fbbfa2679b64 -r e9dcf9066aaa7db5fcbf0ea5ec48d9428ff1f145 cron/parse_builds.py
--- a/cron/parse_builds.py
+++ b/cron/parse_builds.py
@@ -2,7 +2,7 @@
"""
Connects to the URL specified and outputs builds available at that
-DSN in tabular format. USCS Test gateway is used as default.
+DSN in tabular format. UCSC Main gateway is used as default.
build description
"""
@@ -10,7 +10,10 @@
import urllib
import xml.etree.ElementTree as ElementTree
-URL = "http://genome.cse.ucsc.edu/cgi-bin/das/dsn"
+try:
+ URL = sys.argv[1]
+except IndexError:
+ URL = "http://genome.cse.ucsc.edu/cgi-bin/das/dsn"
def getbuilds(url):
try:
@@ -28,7 +31,7 @@
print "?\tunspecified (?)"
sys.exit(1)
- print "#Harvested from http://genome.cse.ucsc.edu/cgi-bin/das/dsn"
+ print "#Harvested from " + URL
print "?\tunspecified (?)"
for dsn in tree:
build = dsn.find("SOURCE").attrib['id']
https://bitbucket.org/galaxy/galaxy-central/commits/5cec4dd844b2/
Changeset: 5cec4dd844b2
User: martenson
Date: 2015-03-02 21:33:43+00:00
Summary: tweak toolbox search to provide better (and more) results
with the inclusion of toolhelp in index and with more versions
of the same tools being massively installed the search results were
inconsistent and inaccurate and incomplete.
addresses https://trello.com/c/6Bvbduci/2486-toolbox-search-is-behaving-wrongly-diffe…
Affected #: 7 files
diff -r e9dcf9066aaa7db5fcbf0ea5ec48d9428ff1f145 -r 5cec4dd844b27d45bc1c31a6c6d0707a67473086 client/galaxy/scripts/galaxy.workflows.js
--- a/client/galaxy/scripts/galaxy.workflows.js
+++ b/client/galaxy/scripts/galaxy.workflows.js
@@ -24,7 +24,7 @@
$(this).addClass("search_active");
// input.addClass(config.loadingClass);
// Add '*' to facilitate partial matching.
- var q = this.value + '*';
+ var q = this.value;
// Stop previous ajax-request
if (this.timer) {
clearTimeout(this.timer);
diff -r e9dcf9066aaa7db5fcbf0ea5ec48d9428ff1f145 -r 5cec4dd844b27d45bc1c31a6c6d0707a67473086 client/galaxy/scripts/mvc/tools.js
--- a/client/galaxy/scripts/mvc/tools.js
+++ b/client/galaxy/scripts/mvc/tools.js
@@ -376,7 +376,7 @@
}
// Do search via AJAX.
- var q = query + '*';
+ var q = query;
// Stop previous ajax-request
if (this.timer) {
clearTimeout(this.timer);
diff -r e9dcf9066aaa7db5fcbf0ea5ec48d9428ff1f145 -r 5cec4dd844b27d45bc1c31a6c6d0707a67473086 lib/galaxy/tools/search/__init__.py
--- a/lib/galaxy/tools/search/__init__.py
+++ b/lib/galaxy/tools/search/__init__.py
@@ -1,18 +1,27 @@
-from galaxy.eggs import require
+"""
+Module for building and searching the index of tools
+installed within this Galaxy.
+"""
+from galaxy import eggs
from galaxy.web.framework.helpers import to_unicode
-require( "Whoosh" )
+eggs.require( "Whoosh" )
from whoosh.filedb.filestore import RamStorage
from whoosh.fields import Schema, STORED, TEXT
from whoosh.scoring import BM25F
from whoosh.qparser import MultifieldParser
-schema = Schema( id=STORED, title=TEXT, description=TEXT, help=TEXT )
-
+schema = Schema( id=STORED,
+ title=TEXT,
+ description=TEXT,
+ section=TEXT,
+ help=TEXT )
+import logging
+log = logging.getLogger( __name__ )
class ToolBoxSearch( object ):
"""
Support searching tools in a toolbox. This implementation uses
- the "whoosh" search library.
+ the Whoosh search library.
"""
def __init__( self, toolbox, index_help=True ):
@@ -26,13 +35,13 @@
self.storage = RamStorage()
self.index = self.storage.create_index( schema )
writer = self.index.writer()
- ## TODO: would also be nice to search section headers.
for id, tool in self.toolbox.tools():
add_doc_kwds = {
"id": id,
- "title": to_unicode(tool.name),
- "description": to_unicode(tool.description),
- "help": to_unicode(""),
+ "title": to_unicode( tool.name ),
+ "description": to_unicode( tool.description ),
+ "section": to_unicode( tool.get_panel_section()[1] if len( tool.get_panel_section() ) == 2 else '' ),
+ "help": to_unicode( "" ),
}
if index_help and tool.help:
try:
@@ -45,13 +54,18 @@
writer.commit()
def search( self, query, return_attribute='id' ):
- # Change field boosts for searcher to place more weight on title, description than help.
+ # Change field boosts for searcher
searcher = self.index.searcher(
weighting=BM25F(
- field_B={ 'title_B': 3, 'description_B': 2, 'help_B': 1 }
+ field_B={ 'title_B': 9,
+ 'section_B': 3,
+ 'description_B': 2,
+ 'help_B': 0.5 }
)
)
- # Set query to search title, description, and help.
- parser = MultifieldParser( [ 'title', 'description', 'help' ], schema=schema )
- results = searcher.search( parser.parse( query ) )
- return [ result[ return_attribute ] for result in results ]
+ # Set query to search title, description, section, and help.
+ parser = MultifieldParser( [ 'title', 'description', 'section', 'help' ], schema=schema )
+ # Perform the search
+ hits = searcher.search( parser.parse( '*' + query + '*' ), limit=20 )
+
+ return [ hit[ return_attribute ] for hit in hits ]
diff -r e9dcf9066aaa7db5fcbf0ea5ec48d9428ff1f145 -r 5cec4dd844b27d45bc1c31a6c6d0707a67473086 static/scripts/galaxy.workflows.js
--- a/static/scripts/galaxy.workflows.js
+++ b/static/scripts/galaxy.workflows.js
@@ -24,7 +24,7 @@
$(this).addClass("search_active");
// input.addClass(config.loadingClass);
// Add '*' to facilitate partial matching.
- var q = this.value + '*';
+ var q = this.value;
// Stop previous ajax-request
if (this.timer) {
clearTimeout(this.timer);
diff -r e9dcf9066aaa7db5fcbf0ea5ec48d9428ff1f145 -r 5cec4dd844b27d45bc1c31a6c6d0707a67473086 static/scripts/mvc/tools.js
--- a/static/scripts/mvc/tools.js
+++ b/static/scripts/mvc/tools.js
@@ -376,7 +376,7 @@
}
// Do search via AJAX.
- var q = query + '*';
+ var q = query;
// Stop previous ajax-request
if (this.timer) {
clearTimeout(this.timer);
diff -r e9dcf9066aaa7db5fcbf0ea5ec48d9428ff1f145 -r 5cec4dd844b27d45bc1c31a6c6d0707a67473086 static/scripts/packed/galaxy.workflows.js
--- a/static/scripts/packed/galaxy.workflows.js
+++ b/static/scripts/packed/galaxy.workflows.js
@@ -1,1 +1,1 @@
-$(function(){if(window.lt_ie_7){show_modal("Browser not supported","Sorry, the workflow editor is not supported for IE6 and below.");return}$("#tool-search-query").click(function(){$(this).focus();$(this).select()}).keyup(function(){$(this).css("font-style","normal");if(this.value.length<3){reset_tool_search(false)}else{if(this.value!=this.lastValue){$(this).addClass("search_active");var g=this.value+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();this.timer=setTimeout(function(){$.get(tool_search_url,{query:g},function(i){$("#search-no-results").hide();$(".toolSectionWrapper").hide();$(".toolSectionWrapper").find(".toolTitle").hide();if(i.length!=0){var h=$.map(i,function(k,j){return"link-"+k});$(h).each(function(j,k){$("[id='"+k+"']").parent().addClass("search_match");$("[id='"+k+"']").parent().show().parent().parent().show().parent().show()});$(".toolPanelLabel").each(function(){var l=$(this);var k=l.next();var j=true;while(k.length!==0&&k.hasClass("toolTitle")){if(k.is(":visible")){j=false;break}else{k=k.next()}}if(j){l.hide()}})}else{$("#search-no-results").show()}$("#search-spinner").hide()},"json")},200)}}this.lastValue=this.value});canvas_manager=new CanvasManager($("#canvas-viewport"),$("#overview"));reset();$.ajax({url:get_datatypes_url,dataType:"json",cache:false,success:function(g){populate_datatype_info(g);$.ajax({url:load_workflow_url,data:{id:workflow_id,_:"true"},dataType:"json",cache:false,success:function(h){reset();workflow.from_simple(h);workflow.has_changes=false;workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview();upgrade_message="";$.each(h.upgrade_messages,function(j,i){upgrade_message+=("<li>Step "+(parseInt(j,10)+1)+": "+workflow.nodes[j].name+"<ul>");$.each(i,function(k,l){upgrade_message+="<li>"+l+"</li>"});upgrade_message+="</ul></li>"});if(upgrade_message){show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal})}else{hide_modal()}show_workflow_parameters()},beforeSubmit:function(h){show_message("Loading workflow","progress")}})}});$(document).ajaxStart(function(){active_ajax_call=true;$(document).bind("ajaxStop.global",function(){active_ajax_call=false})});$(document).ajaxError(function(i,g){var h=g.responseText||g.statusText||"Could not connect to server";show_modal("Server error",h,{"Ignore error":hide_modal});return false});make_popupmenu($("#workflow-options-button"),{Save:save_current_workflow,Run:function(){window.location=run_workflow_url},"Edit Attributes":c,"Auto Re-layout":f,Close:close_editor});function b(){workflow.clear_active_node();$(".right-content").hide();var j="";for(var h in workflow.nodes){var i=workflow.nodes[h];if(i.type=="tool"){j+="<div class='toolForm' style='margin-bottom:5px;'><div class='toolFormTitle'>Step "+i.id+" - "+i.name+"</div>";for(var k in i.output_terminals){var g=i.output_terminals[k];if($.inArray(g.name,i.workflow_outputs)!=-1){j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' checked /></p>"}else{j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' /></p>"}}j+="</div>"}}$("#output-fill-area").html(j);$("#output-fill-area input").bind("click",function(){var n=this.name.split("|")[0];var l=this.name.split("|")[1];if(this.checked){if($.inArray(l,workflow.nodes[n].workflow_outputs)==-1){workflow.nodes[n].workflow_outputs.push(l)}}else{while($.inArray(l,workflow.nodes[n].workflow_outputs)!=-1){var m=$.inArray(l,workflow.nodes[n].workflow_outputs);workflow.nodes[n].workflow_outputs=workflow.nodes[n].workflow_outputs.slice(0,m).concat(workflow.nodes[n].workflow_outputs.slice(m+1))}}workflow.has_changes=true});$("#workflow-output-area").show()}function f(){workflow.layout();workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview()}function c(){workflow.clear_active_node();$(".right-content").hide();$("#edit-attributes").show()}overview_size=$.jStorage.get("overview-size");if(overview_size!==undefined){$("#overview-border").css({width:overview_size,height:overview_size})}if($.jStorage.get("overview-off")){d()}else{e()}$("#overview-border").bind("dragend",function(h,j){var k=$(this).offsetParent();var i=k.offset();var g=Math.max(k.width()-(j.offsetX-i.left),k.height()-(j.offsetY-i.top));$.jStorage.set("overview-size",g+"px")});function e(){$.jStorage.set("overview-off",false);$("#overview-border").css("right","0px");$("#close-viewport").css("background-position","0px 0px")}function d(){$.jStorage.set("overview-off",true);$("#overview-border").css("right","20000px");$("#close-viewport").css("background-position","12px 0px")}$("#close-viewport").click(function(){if($("#overview-border").css("right")==="0px"){d()}else{e()}});window.onbeforeunload=function(){if(workflow&&workflow.has_changes){return"There are unsaved changes to your workflow which will be lost."}};$("div.toolSectionBody").hide();$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var a=null;$("div.toolSectionTitle").each(function(){var g=$(this).next("div.toolSectionBody");$(this).click(function(){if(g.is(":hidden")){if(a){a.slideUp("fast")}a=g;g.slideDown("fast")}else{g.slideUp("fast");a=null}})});async_save_text("workflow-name","workflow-name",rename_async_url,"new_name");$("#workflow-tag").click(function(){$(".tag-area").click();return false});async_save_text("workflow-annotation","workflow-annotation",annotate_async_url,"new_annotation",25,true,4)});function reset(){if(workflow){workflow.remove_all()}workflow=new Workflow($("#canvas-container"))}function scroll_to_nodes(){var a=$("#canvas-viewport");var d=$("#canvas-container");var c,b;if(d.width()<a.width()){b=(a.width()-d.width())/2}else{b=0}if(d.height()<a.height()){c=(a.height()-d.height())/2}else{c=0}d.css({left:b,top:c})}function add_node_for_tool(b,a){node=add_node("tool",a,b);$.ajax({url:get_new_module_info_url,data:{type:"tool",tool_id:b,_:"true"},global:false,dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status===0){c+=", server unavailable"}node.error(c)}})}function add_node_for_module(a,b){node=add_node(a,b);$.ajax({url:get_new_module_info_url,data:{type:a,_:"true"},dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status==0){c+=", server unavailable"}node.error(c)}})}function display_pja(b,a){$("#pja_container").append(get_pja_form(b,a));$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text();$(this).closest(".toolForm").remove();delete workflow.active_node.post_job_actions[action_to_rem];workflow.active_form_has_changes=true})}function display_pja_list(){return pja_list}function display_file_list(b){addlist="<select id='node_data_list' name='node_data_list'>";for(var a in b.output_terminals){addlist+="<option value='"+a+"'>"+a+"</option>"}addlist+="</select>";return addlist}function new_pja(d,b,a){if(a.post_job_actions===undefined){a.post_job_actions={}}if(a.post_job_actions[d+b]===undefined){var c={};c.action_type=d;c.output_name=b;a.post_job_actions[d+b]=null;a.post_job_actions[d+b]=c;display_pja(c,a);workflow.active_form_has_changes=true;return true}else{return false}}function show_workflow_parameters(){var c=/\$\{.+?\}/g;var b=[];var f=$("#workflow-parameters-container");var e=$("#workflow-parameters-box");var a="";var d=[];$.each(workflow.nodes,function(g,h){var i=h.form_html.match(c);if(i){d=d.concat(i)}if(h.post_job_actions){$.each(h.post_job_actions,function(j,l){if(l.action_arguments){$.each(l.action_arguments,function(m,n){var o=n.match(c);if(o){d=d.concat(o)}})}});if(d){$.each(d,function(j,l){if($.inArray(l,b)===-1){b.push(l)}})}}});if(b&&b.length!==0){$.each(b,function(g,h){a+="<div>"+h.substring(2,h.length-1)+"</div>"});f.html(a);e.show()}else{f.html(a);e.hide()}}function show_form_for_tool(c,b){$(".right-content").hide();$("#right-content").show().html(c);if(b){$("#right-content").find(".toolForm:first").after("<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Attributes</div><div class='form-row'><label>Annotation / Notes:</label><div style='margin-right: 10px;'><textarea name='annotation' rows='3' style='width: 100%'>"+b.annotation+"</textarea><div class='toolParamHelp'>Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div></div></div></div>")}if(b&&b.type=="tool"){pjastr="<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Actions</div><div class='form-row'> "+display_pja_list()+" <br/> "+display_file_list(b)+" <div class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div></div><div class='form-row'><div style='margin-right: 10px;'><span id='pja_container'></span>";pjastr+="<div class='toolParamHelp'>Add actions to this step; actions are applied when this workflow step completes.</div></div></div></div>";$("#right-content").find(".toolForm").after(pjastr);for(var a in b.post_job_actions){if(a!="undefined"){display_pja(b.post_job_actions[a],b)}}$("#add_pja").click(function(){new_pja($("#new_pja_list").val(),$("#node_data_list").val(),b)})}$("#right-content").find("form").ajaxForm({type:"POST",dataType:"json",success:function(d){workflow.active_form_has_changes=false;b.update_field_data(d);show_workflow_parameters()},beforeSubmit:function(d){d.push({name:"tool_state",value:b.tool_state});d.push({name:"_",value:"true"})}}).each(function(){var d=this;$(this).find("select[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find("input[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find(".popupmenu").each(function(){var g=$(this).parents("div.form-row").attr("id");var e=$('<a class="popup-arrow" id="popup-arrow-for-'+g+'">▼</a>');var f={};$(this).find("button").each(function(){var h=$(this).attr("name");var i=$(this).attr("value");f[$(this).text()]=function(){$(d).append("<input type='hidden' name='"+h+"' value='"+i+"' />").submit()}});e.insertAfter(this);$(this).remove();make_popupmenu(e,f)});$(this).find("input,textarea,select").each(function(){$(this).bind("focus click",function(){workflow.active_form_has_changes=true})})})}var close_editor=function(){workflow.check_changes_in_active_form();if(workflow&&workflow.has_changes){do_close=function(){window.onbeforeunload=undefined;window.document.location=workflow_index_url};show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){save_current_workflow(null,do_close)}},{"Don't Save":do_close})}else{window.document.location=workflow_index_url}};var save_current_workflow=function(b,c){show_message("Saving workflow","progress");workflow.check_changes_in_active_form();if(!workflow.has_changes){hide_modal();if(c){c()}return}workflow.rectify_workflow_outputs();var a=function(d){$.ajax({url:save_workflow_url,type:"POST",data:{id:workflow_id,workflow_data:function(){return JSON.stringify(workflow.to_simple())},_:"true"},dataType:"json",success:function(g){var e=$("<div></div>").text(g.message);if(g.errors){e.addClass("warningmark");var f=$("<ul/>");$.each(g.errors,function(j,h){$("<li></li>").text(h).appendTo(f)});e.append(f)}else{e.addClass("donemark")}workflow.name=g.name;workflow.has_changes=false;workflow.stored=true;show_workflow_parameters();if(g.errors){show_modal("Saving workflow",e,{Ok:hide_modal})}else{if(d){d()}hide_modal()}}})};if(active_ajax_call){$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow");a();$(document).unbind("ajaxStop.save_workflow");active_ajax_call=false})}else{a(c)}};
\ No newline at end of file
+$(function(){if(window.lt_ie_7){show_modal("Browser not supported","Sorry, the workflow editor is not supported for IE6 and below.");return}$("#tool-search-query").click(function(){$(this).focus();$(this).select()}).keyup(function(){$(this).css("font-style","normal");if(this.value.length<3){reset_tool_search(false)}else{if(this.value!=this.lastValue){$(this).addClass("search_active");var g=this.value;if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();this.timer=setTimeout(function(){$.get(tool_search_url,{query:g},function(i){$("#search-no-results").hide();$(".toolSectionWrapper").hide();$(".toolSectionWrapper").find(".toolTitle").hide();if(i.length!=0){var h=$.map(i,function(k,j){return"link-"+k});$(h).each(function(j,k){$("[id='"+k+"']").parent().addClass("search_match");$("[id='"+k+"']").parent().show().parent().parent().show().parent().show()});$(".toolPanelLabel").each(function(){var l=$(this);var k=l.next();var j=true;while(k.length!==0&&k.hasClass("toolTitle")){if(k.is(":visible")){j=false;break}else{k=k.next()}}if(j){l.hide()}})}else{$("#search-no-results").show()}$("#search-spinner").hide()},"json")},200)}}this.lastValue=this.value});canvas_manager=new CanvasManager($("#canvas-viewport"),$("#overview"));reset();$.ajax({url:get_datatypes_url,dataType:"json",cache:false,success:function(g){populate_datatype_info(g);$.ajax({url:load_workflow_url,data:{id:workflow_id,_:"true"},dataType:"json",cache:false,success:function(h){reset();workflow.from_simple(h);workflow.has_changes=false;workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview();upgrade_message="";$.each(h.upgrade_messages,function(j,i){upgrade_message+=("<li>Step "+(parseInt(j,10)+1)+": "+workflow.nodes[j].name+"<ul>");$.each(i,function(k,l){upgrade_message+="<li>"+l+"</li>"});upgrade_message+="</ul></li>"});if(upgrade_message){show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal})}else{hide_modal()}show_workflow_parameters()},beforeSubmit:function(h){show_message("Loading workflow","progress")}})}});$(document).ajaxStart(function(){active_ajax_call=true;$(document).bind("ajaxStop.global",function(){active_ajax_call=false})});$(document).ajaxError(function(i,g){var h=g.responseText||g.statusText||"Could not connect to server";show_modal("Server error",h,{"Ignore error":hide_modal});return false});make_popupmenu($("#workflow-options-button"),{Save:save_current_workflow,Run:function(){window.location=run_workflow_url},"Edit Attributes":c,"Auto Re-layout":f,Close:close_editor});function b(){workflow.clear_active_node();$(".right-content").hide();var j="";for(var h in workflow.nodes){var i=workflow.nodes[h];if(i.type=="tool"){j+="<div class='toolForm' style='margin-bottom:5px;'><div class='toolFormTitle'>Step "+i.id+" - "+i.name+"</div>";for(var k in i.output_terminals){var g=i.output_terminals[k];if($.inArray(g.name,i.workflow_outputs)!=-1){j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' checked /></p>"}else{j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' /></p>"}}j+="</div>"}}$("#output-fill-area").html(j);$("#output-fill-area input").bind("click",function(){var n=this.name.split("|")[0];var l=this.name.split("|")[1];if(this.checked){if($.inArray(l,workflow.nodes[n].workflow_outputs)==-1){workflow.nodes[n].workflow_outputs.push(l)}}else{while($.inArray(l,workflow.nodes[n].workflow_outputs)!=-1){var m=$.inArray(l,workflow.nodes[n].workflow_outputs);workflow.nodes[n].workflow_outputs=workflow.nodes[n].workflow_outputs.slice(0,m).concat(workflow.nodes[n].workflow_outputs.slice(m+1))}}workflow.has_changes=true});$("#workflow-output-area").show()}function f(){workflow.layout();workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview()}function c(){workflow.clear_active_node();$(".right-content").hide();$("#edit-attributes").show()}overview_size=$.jStorage.get("overview-size");if(overview_size!==undefined){$("#overview-border").css({width:overview_size,height:overview_size})}if($.jStorage.get("overview-off")){d()}else{e()}$("#overview-border").bind("dragend",function(h,j){var k=$(this).offsetParent();var i=k.offset();var g=Math.max(k.width()-(j.offsetX-i.left),k.height()-(j.offsetY-i.top));$.jStorage.set("overview-size",g+"px")});function e(){$.jStorage.set("overview-off",false);$("#overview-border").css("right","0px");$("#close-viewport").css("background-position","0px 0px")}function d(){$.jStorage.set("overview-off",true);$("#overview-border").css("right","20000px");$("#close-viewport").css("background-position","12px 0px")}$("#close-viewport").click(function(){if($("#overview-border").css("right")==="0px"){d()}else{e()}});window.onbeforeunload=function(){if(workflow&&workflow.has_changes){return"There are unsaved changes to your workflow which will be lost."}};$("div.toolSectionBody").hide();$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var a=null;$("div.toolSectionTitle").each(function(){var g=$(this).next("div.toolSectionBody");$(this).click(function(){if(g.is(":hidden")){if(a){a.slideUp("fast")}a=g;g.slideDown("fast")}else{g.slideUp("fast");a=null}})});async_save_text("workflow-name","workflow-name",rename_async_url,"new_name");$("#workflow-tag").click(function(){$(".tag-area").click();return false});async_save_text("workflow-annotation","workflow-annotation",annotate_async_url,"new_annotation",25,true,4)});function reset(){if(workflow){workflow.remove_all()}workflow=new Workflow($("#canvas-container"))}function scroll_to_nodes(){var a=$("#canvas-viewport");var d=$("#canvas-container");var c,b;if(d.width()<a.width()){b=(a.width()-d.width())/2}else{b=0}if(d.height()<a.height()){c=(a.height()-d.height())/2}else{c=0}d.css({left:b,top:c})}function add_node_for_tool(b,a){node=add_node("tool",a,b);$.ajax({url:get_new_module_info_url,data:{type:"tool",tool_id:b,_:"true"},global:false,dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status===0){c+=", server unavailable"}node.error(c)}})}function add_node_for_module(a,b){node=add_node(a,b);$.ajax({url:get_new_module_info_url,data:{type:a,_:"true"},dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status==0){c+=", server unavailable"}node.error(c)}})}function display_pja(b,a){$("#pja_container").append(get_pja_form(b,a));$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text();$(this).closest(".toolForm").remove();delete workflow.active_node.post_job_actions[action_to_rem];workflow.active_form_has_changes=true})}function display_pja_list(){return pja_list}function display_file_list(b){addlist="<select id='node_data_list' name='node_data_list'>";for(var a in b.output_terminals){addlist+="<option value='"+a+"'>"+a+"</option>"}addlist+="</select>";return addlist}function new_pja(d,b,a){if(a.post_job_actions===undefined){a.post_job_actions={}}if(a.post_job_actions[d+b]===undefined){var c={};c.action_type=d;c.output_name=b;a.post_job_actions[d+b]=null;a.post_job_actions[d+b]=c;display_pja(c,a);workflow.active_form_has_changes=true;return true}else{return false}}function show_workflow_parameters(){var c=/\$\{.+?\}/g;var b=[];var f=$("#workflow-parameters-container");var e=$("#workflow-parameters-box");var a="";var d=[];$.each(workflow.nodes,function(g,h){var i=h.form_html.match(c);if(i){d=d.concat(i)}if(h.post_job_actions){$.each(h.post_job_actions,function(j,l){if(l.action_arguments){$.each(l.action_arguments,function(m,n){var 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class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div></div><div class='form-row'><div style='margin-right: 10px;'><span id='pja_container'></span>";pjastr+="<div class='toolParamHelp'>Add actions to this step; actions are applied when this workflow step completes.</div></div></div></div>";$("#right-content").find(".toolForm").after(pjastr);for(var a in b.post_job_actions){if(a!="undefined"){display_pja(b.post_job_actions[a],b)}}$("#add_pja").click(function(){new_pja($("#new_pja_list").val(),$("#node_data_list").val(),b)})}$("#right-content").find("form").ajaxForm({type:"POST",dataType:"json",success:function(d){workflow.active_form_has_changes=false;b.update_field_data(d);show_workflow_parameters()},beforeSubmit:function(d){d.push({name:"tool_state",value:b.tool_state});d.push({name:"_",value:"true"})}}).each(function(){var d=this;$(this).find("select[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find("input[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find(".popupmenu").each(function(){var g=$(this).parents("div.form-row").attr("id");var e=$('<a class="popup-arrow" id="popup-arrow-for-'+g+'">▼</a>');var f={};$(this).find("button").each(function(){var h=$(this).attr("name");var i=$(this).attr("value");f[$(this).text()]=function(){$(d).append("<input type='hidden' name='"+h+"' value='"+i+"' />").submit()}});e.insertAfter(this);$(this).remove();make_popupmenu(e,f)});$(this).find("input,textarea,select").each(function(){$(this).bind("focus click",function(){workflow.active_form_has_changes=true})})})}var close_editor=function(){workflow.check_changes_in_active_form();if(workflow&&workflow.has_changes){do_close=function(){window.onbeforeunload=undefined;window.document.location=workflow_index_url};show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){save_current_workflow(null,do_close)}},{"Don't Save":do_close})}else{window.document.location=workflow_index_url}};var save_current_workflow=function(b,c){show_message("Saving workflow","progress");workflow.check_changes_in_active_form();if(!workflow.has_changes){hide_modal();if(c){c()}return}workflow.rectify_workflow_outputs();var a=function(d){$.ajax({url:save_workflow_url,type:"POST",data:{id:workflow_id,workflow_data:function(){return JSON.stringify(workflow.to_simple())},_:"true"},dataType:"json",success:function(g){var e=$("<div></div>").text(g.message);if(g.errors){e.addClass("warningmark");var f=$("<ul/>");$.each(g.errors,function(j,h){$("<li></li>").text(h).appendTo(f)});e.append(f)}else{e.addClass("donemark")}workflow.name=g.name;workflow.has_changes=false;workflow.stored=true;show_workflow_parameters();if(g.errors){show_modal("Saving workflow",e,{Ok:hide_modal})}else{if(d){d()}hide_modal()}}})};if(active_ajax_call){$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow");a();$(document).unbind("ajaxStop.save_workflow");active_ajax_call=false})}else{a(c)}};
\ No newline at end of file
diff -r e9dcf9066aaa7db5fcbf0ea5ec48d9428ff1f145 -r 5cec4dd844b27d45bc1c31a6c6d0707a67473086 static/scripts/packed/mvc/tools.js
--- a/static/scripts/packed/mvc/tools.js
+++ b/static/scripts/packed/mvc/tools.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/trackster/util","mvc/data","libs/lunr"],function(y,a,z,s){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(A){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(A){this.set("value",A||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(A){this.set("value",parseInt(A,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(A){this.set("value",parseFloat(A))}});var u=e.extend({get_samples:function(){return y.map(this.get("options"),function(A){return A[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:u};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(A){this.set("inputs",new i(y.map(A.inputs,function(B){var C=e.subModelTypes[B.type]||e;return new C(B)})))},toJSON:function(){var A=Backbone.Model.prototype.toJSON.call(this);A.inputs=this.get("inputs").map(function(B){return B.toJSON()});return A},remove_inputs:function(B){var A=this,C=A.get("inputs").filter(function(D){return(B.indexOf(D.get("type"))!==-1)});A.get("inputs").remove(C)},copy:function(B){var C=new j(this.toJSON());if(B){var A=new Backbone.Collection();C.get("inputs").each(function(D){if(D.get_samples()){A.push(D)}});C.set("inputs",A)}return C},apply_search_results:function(A){(y.indexOf(A,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(A,B){this.get("inputs").find(function(C){return C.get("name")===A}).set("value",B)},set_input_values:function(B){var A=this;y.each(y.keys(B),function(C){A.set_input_value(C,B[C])})},run:function(){return this._run()},rerun:function(B,A){return this._run({action:"rerun",target_dataset_id:B.id,regions:A})},get_inputs_dict:function(){var A={};this.get("inputs").each(function(B){A[B.get("name")]=B.get("value")});return A},_run:function(C){var D=y.extend({tool_id:this.id,inputs:this.get_inputs_dict()},C);var B=$.Deferred(),A=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(D),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(E){return E!=="pending"}});$.when(A.go()).then(function(E){B.resolve(new z.DatasetCollection().reset(E))});return B}});y.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var w=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){y.each(this.attributes.elems,function(A){A.show()});this.show();this.set("open",false)},apply_search_results:function(B){var C=true,A;y.each(this.attributes.elems,function(D){if(D instanceof w){A=D;A.hide()}else{if(D instanceof j){if(D.apply_search_results(B)){C=false;if(A){A.show()}}}}});if(C){this.hide()}else{this.show();this.set("open",true)}}});y.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var C=this.attributes.query;if(C.length<this.attributes.min_chars_for_search){this.set("results",null);return}var B=C+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var A=this;this.timer=setTimeout(function(){$.get(A.attributes.search_url,{query:B},function(D){A.set("results",D);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});y.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(A){this.attributes.tool_search=A.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=A.tools;this.attributes.layout=new Backbone.Collection(this.parse(A.layout))},parse:function(B){var A=this,C=function(F){var E=F.model_class;if(E.indexOf("Tool")===E.length-4){return A.attributes.tools.get(F.id)}else{if(E==="ToolSection"){var D=y.map(F.elems,C);F.elems=D;return new l(F)}else{if(E==="ToolSectionLabel"){return new w(F)}}}};return y.map(B,C)},clear_search_results:function(){this.get("layout").each(function(A){if(A instanceof l){A.clear_search_results()}else{A.show()}})},apply_search_results:function(){var B=this.get("tool_search").get("results");if(B===null){this.clear_search_results();return}var A=null;this.get("layout").each(function(C){if(C instanceof w){A=C;A.hide()}else{if(C instanceof j){if(C.apply_search_results(B)){if(A){A.show()}}}else{A=null;C.apply_search_results(B)}}})}});var t=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=t.extend({tagName:"div",render:function(){var A=$("<div/>");A.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){A.find("a").on("click",function(B){B.preventDefault();Galaxy.upload.show()})}this.$el.append(A);return this}});var b=t.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=t.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){t.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var A=this.$el.find(".toolSectionBody");y.each(this.model.attributes.elems,function(B){if(B instanceof j){var C=new m({model:B,className:"toolTitle"});C.render();A.append(C.$el)}else{if(B instanceof w){var D=new b({model:B});D.render();A.append(D.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(A){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===A.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var x=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var A=this;var B=new p({model:this.model.get("tool_search")});B.render();A.$el.append(B.$el);this.model.get("layout").each(function(D){if(D instanceof l){var C=new r({model:D});C.render();A.$el.append(C.$el)}else{if(D instanceof j){var E=new m({model:D,className:"toolTitleNoSection"});E.render();A.$el.append(E.$el)}else{if(D instanceof w){var F=new b({model:D});F.render();A.$el.append(F.$el)}}}});A.$el.find("a.tool-link").click(function(E){var D=$(this).attr("class").split(/\s+/)[0],C=A.model.get("tools").get(D);A.trigger("tool_link_click",E,C)});return this},handle_search_results:function(){var A=this.model.get("tool_search").get("results");if(A&&A.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var v=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new x({collection:this.collection});this.tool_form_view=new v()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var A=this;this.tool_panel_view.on("tool_link_click",function(C,B){C.preventDefault();A.show_tool(B)})},show_tool:function(B){var A=this;B.fetch().done(function(){A.tool_form_view.model=B;A.tool_form_view.render();A.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:u,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:x,ToolFormView:v}});
\ No newline at end of file
+define(["libs/underscore","viz/trackster/util","mvc/data","libs/lunr"],function(y,a,z,s){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(A){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(A){this.set("value",A||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(A){this.set("value",parseInt(A,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(A){this.set("value",parseFloat(A))}});var u=e.extend({get_samples:function(){return y.map(this.get("options"),function(A){return A[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:u};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(A){this.set("inputs",new i(y.map(A.inputs,function(B){var C=e.subModelTypes[B.type]||e;return new C(B)})))},toJSON:function(){var A=Backbone.Model.prototype.toJSON.call(this);A.inputs=this.get("inputs").map(function(B){return B.toJSON()});return A},remove_inputs:function(B){var A=this,C=A.get("inputs").filter(function(D){return(B.indexOf(D.get("type"))!==-1)});A.get("inputs").remove(C)},copy:function(B){var C=new j(this.toJSON());if(B){var A=new Backbone.Collection();C.get("inputs").each(function(D){if(D.get_samples()){A.push(D)}});C.set("inputs",A)}return C},apply_search_results:function(A){(y.indexOf(A,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(A,B){this.get("inputs").find(function(C){return C.get("name")===A}).set("value",B)},set_input_values:function(B){var A=this;y.each(y.keys(B),function(C){A.set_input_value(C,B[C])})},run:function(){return this._run()},rerun:function(B,A){return this._run({action:"rerun",target_dataset_id:B.id,regions:A})},get_inputs_dict:function(){var A={};this.get("inputs").each(function(B){A[B.get("name")]=B.get("value")});return A},_run:function(C){var D=y.extend({tool_id:this.id,inputs:this.get_inputs_dict()},C);var B=$.Deferred(),A=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(D),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(E){return E!=="pending"}});$.when(A.go()).then(function(E){B.resolve(new z.DatasetCollection().reset(E))});return B}});y.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var w=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){y.each(this.attributes.elems,function(A){A.show()});this.show();this.set("open",false)},apply_search_results:function(B){var C=true,A;y.each(this.attributes.elems,function(D){if(D instanceof w){A=D;A.hide()}else{if(D instanceof j){if(D.apply_search_results(B)){C=false;if(A){A.show()}}}}});if(C){this.hide()}else{this.show();this.set("open",true)}}});y.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var C=this.attributes.query;if(C.length<this.attributes.min_chars_for_search){this.set("results",null);return}var B=C;if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var A=this;this.timer=setTimeout(function(){$.get(A.attributes.search_url,{query:B},function(D){A.set("results",D);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});y.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(A){this.attributes.tool_search=A.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=A.tools;this.attributes.layout=new Backbone.Collection(this.parse(A.layout))},parse:function(B){var A=this,C=function(F){var E=F.model_class;if(E.indexOf("Tool")===E.length-4){return A.attributes.tools.get(F.id)}else{if(E==="ToolSection"){var D=y.map(F.elems,C);F.elems=D;return new l(F)}else{if(E==="ToolSectionLabel"){return new w(F)}}}};return y.map(B,C)},clear_search_results:function(){this.get("layout").each(function(A){if(A instanceof l){A.clear_search_results()}else{A.show()}})},apply_search_results:function(){var B=this.get("tool_search").get("results");if(B===null){this.clear_search_results();return}var A=null;this.get("layout").each(function(C){if(C instanceof w){A=C;A.hide()}else{if(C instanceof j){if(C.apply_search_results(B)){if(A){A.show()}}}else{A=null;C.apply_search_results(B)}}})}});var t=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=t.extend({tagName:"div",render:function(){var A=$("<div/>");A.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){A.find("a").on("click",function(B){B.preventDefault();Galaxy.upload.show()})}this.$el.append(A);return this}});var b=t.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=t.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){t.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var A=this.$el.find(".toolSectionBody");y.each(this.model.attributes.elems,function(B){if(B instanceof j){var C=new m({model:B,className:"toolTitle"});C.render();A.append(C.$el)}else{if(B instanceof w){var D=new b({model:B});D.render();A.append(D.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(A){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===A.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var x=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var A=this;var B=new p({model:this.model.get("tool_search")});B.render();A.$el.append(B.$el);this.model.get("layout").each(function(D){if(D instanceof l){var C=new r({model:D});C.render();A.$el.append(C.$el)}else{if(D instanceof j){var E=new m({model:D,className:"toolTitleNoSection"});E.render();A.$el.append(E.$el)}else{if(D instanceof w){var F=new b({model:D});F.render();A.$el.append(F.$el)}}}});A.$el.find("a.tool-link").click(function(E){var D=$(this).attr("class").split(/\s+/)[0],C=A.model.get("tools").get(D);A.trigger("tool_link_click",E,C)});return this},handle_search_results:function(){var A=this.model.get("tool_search").get("results");if(A&&A.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var v=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new x({collection:this.collection});this.tool_form_view=new v()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var A=this;this.tool_panel_view.on("tool_link_click",function(C,B){C.preventDefault();A.show_tool(B)})},show_tool:function(B){var A=this;B.fetch().done(function(){A.tool_form_view.model=B;A.tool_form_view.render();A.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:u,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:x,ToolFormView:v}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/14f402d4a683/
Changeset: 14f402d4a683
User: martenson
Date: 2015-03-02 21:39:48+00:00
Summary: increase toolbox search delay
log search terms
Affected #: 3 files
diff -r 5cec4dd844b27d45bc1c31a6c6d0707a67473086 -r 14f402d4a6830e984a58bf626be2f8c40ae91b5a client/galaxy/scripts/mvc/tools.js
--- a/client/galaxy/scripts/mvc/tools.js
+++ b/client/galaxy/scripts/mvc/tools.js
@@ -385,13 +385,15 @@
$("#search-clear-btn").hide();
$("#search-spinner").show();
var self = this;
+ // log the search to analytics
+ ga( 'send', 'pageview', galaxy_config.root + '?q=' + q );
this.timer = setTimeout(function () {
$.get(self.attributes.search_url, { query: q }, function (data) {
self.set("results", data);
$("#search-spinner").hide();
$("#search-clear-btn").show();
}, "json" );
- }, 200 );
+ }, 400 );
},
clear_search: function() {
diff -r 5cec4dd844b27d45bc1c31a6c6d0707a67473086 -r 14f402d4a6830e984a58bf626be2f8c40ae91b5a static/scripts/mvc/tools.js
--- a/static/scripts/mvc/tools.js
+++ b/static/scripts/mvc/tools.js
@@ -385,13 +385,15 @@
$("#search-clear-btn").hide();
$("#search-spinner").show();
var self = this;
+ // log the search to analytics
+ ga( 'send', 'pageview', galaxy_config.root + '?q=' + q );
this.timer = setTimeout(function () {
$.get(self.attributes.search_url, { query: q }, function (data) {
self.set("results", data);
$("#search-spinner").hide();
$("#search-clear-btn").show();
}, "json" );
- }, 200 );
+ }, 400 );
},
clear_search: function() {
diff -r 5cec4dd844b27d45bc1c31a6c6d0707a67473086 -r 14f402d4a6830e984a58bf626be2f8c40ae91b5a static/scripts/packed/mvc/tools.js
--- a/static/scripts/packed/mvc/tools.js
+++ b/static/scripts/packed/mvc/tools.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/trackster/util","mvc/data","libs/lunr"],function(y,a,z,s){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(A){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(A){this.set("value",A||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(A){this.set("value",parseInt(A,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(A){this.set("value",parseFloat(A))}});var u=e.extend({get_samples:function(){return y.map(this.get("options"),function(A){return A[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:u};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(A){this.set("inputs",new i(y.map(A.inputs,function(B){var C=e.subModelTypes[B.type]||e;return new C(B)})))},toJSON:function(){var A=Backbone.Model.prototype.toJSON.call(this);A.inputs=this.get("inputs").map(function(B){return B.toJSON()});return A},remove_inputs:function(B){var A=this,C=A.get("inputs").filter(function(D){return(B.indexOf(D.get("type"))!==-1)});A.get("inputs").remove(C)},copy:function(B){var C=new j(this.toJSON());if(B){var A=new Backbone.Collection();C.get("inputs").each(function(D){if(D.get_samples()){A.push(D)}});C.set("inputs",A)}return C},apply_search_results:function(A){(y.indexOf(A,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(A,B){this.get("inputs").find(function(C){return C.get("name")===A}).set("value",B)},set_input_values:function(B){var A=this;y.each(y.keys(B),function(C){A.set_input_value(C,B[C])})},run:function(){return this._run()},rerun:function(B,A){return this._run({action:"rerun",target_dataset_id:B.id,regions:A})},get_inputs_dict:function(){var A={};this.get("inputs").each(function(B){A[B.get("name")]=B.get("value")});return A},_run:function(C){var D=y.extend({tool_id:this.id,inputs:this.get_inputs_dict()},C);var B=$.Deferred(),A=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(D),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(E){return E!=="pending"}});$.when(A.go()).then(function(E){B.resolve(new z.DatasetCollection().reset(E))});return B}});y.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var w=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){y.each(this.attributes.elems,function(A){A.show()});this.show();this.set("open",false)},apply_search_results:function(B){var C=true,A;y.each(this.attributes.elems,function(D){if(D instanceof w){A=D;A.hide()}else{if(D instanceof j){if(D.apply_search_results(B)){C=false;if(A){A.show()}}}}});if(C){this.hide()}else{this.show();this.set("open",true)}}});y.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var C=this.attributes.query;if(C.length<this.attributes.min_chars_for_search){this.set("results",null);return}var B=C;if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var A=this;this.timer=setTimeout(function(){$.get(A.attributes.search_url,{query:B},function(D){A.set("results",D);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});y.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(A){this.attributes.tool_search=A.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=A.tools;this.attributes.layout=new Backbone.Collection(this.parse(A.layout))},parse:function(B){var A=this,C=function(F){var E=F.model_class;if(E.indexOf("Tool")===E.length-4){return A.attributes.tools.get(F.id)}else{if(E==="ToolSection"){var D=y.map(F.elems,C);F.elems=D;return new l(F)}else{if(E==="ToolSectionLabel"){return new w(F)}}}};return y.map(B,C)},clear_search_results:function(){this.get("layout").each(function(A){if(A instanceof l){A.clear_search_results()}else{A.show()}})},apply_search_results:function(){var B=this.get("tool_search").get("results");if(B===null){this.clear_search_results();return}var A=null;this.get("layout").each(function(C){if(C instanceof w){A=C;A.hide()}else{if(C instanceof j){if(C.apply_search_results(B)){if(A){A.show()}}}else{A=null;C.apply_search_results(B)}}})}});var t=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=t.extend({tagName:"div",render:function(){var A=$("<div/>");A.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){A.find("a").on("click",function(B){B.preventDefault();Galaxy.upload.show()})}this.$el.append(A);return this}});var b=t.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=t.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){t.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var A=this.$el.find(".toolSectionBody");y.each(this.model.attributes.elems,function(B){if(B instanceof j){var C=new m({model:B,className:"toolTitle"});C.render();A.append(C.$el)}else{if(B instanceof w){var D=new b({model:B});D.render();A.append(D.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(A){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===A.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var x=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var A=this;var B=new p({model:this.model.get("tool_search")});B.render();A.$el.append(B.$el);this.model.get("layout").each(function(D){if(D instanceof l){var C=new r({model:D});C.render();A.$el.append(C.$el)}else{if(D instanceof j){var E=new m({model:D,className:"toolTitleNoSection"});E.render();A.$el.append(E.$el)}else{if(D instanceof w){var F=new b({model:D});F.render();A.$el.append(F.$el)}}}});A.$el.find("a.tool-link").click(function(E){var D=$(this).attr("class").split(/\s+/)[0],C=A.model.get("tools").get(D);A.trigger("tool_link_click",E,C)});return this},handle_search_results:function(){var A=this.model.get("tool_search").get("results");if(A&&A.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var v=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new x({collection:this.collection});this.tool_form_view=new v()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var A=this;this.tool_panel_view.on("tool_link_click",function(C,B){C.preventDefault();A.show_tool(B)})},show_tool:function(B){var A=this;B.fetch().done(function(){A.tool_form_view.model=B;A.tool_form_view.render();A.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:u,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:x,ToolFormView:v}});
\ No newline at end of file
+define(["libs/underscore","viz/trackster/util","mvc/data","libs/lunr"],function(y,a,z,s){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(A){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(A){this.set("value",A||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(A){this.set("value",parseInt(A,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(A){this.set("value",parseFloat(A))}});var u=e.extend({get_samples:function(){return y.map(this.get("options"),function(A){return A[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:u};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(A){this.set("inputs",new i(y.map(A.inputs,function(B){var C=e.subModelTypes[B.type]||e;return new C(B)})))},toJSON:function(){var A=Backbone.Model.prototype.toJSON.call(this);A.inputs=this.get("inputs").map(function(B){return B.toJSON()});return A},remove_inputs:function(B){var A=this,C=A.get("inputs").filter(function(D){return(B.indexOf(D.get("type"))!==-1)});A.get("inputs").remove(C)},copy:function(B){var C=new j(this.toJSON());if(B){var A=new Backbone.Collection();C.get("inputs").each(function(D){if(D.get_samples()){A.push(D)}});C.set("inputs",A)}return C},apply_search_results:function(A){(y.indexOf(A,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(A,B){this.get("inputs").find(function(C){return C.get("name")===A}).set("value",B)},set_input_values:function(B){var A=this;y.each(y.keys(B),function(C){A.set_input_value(C,B[C])})},run:function(){return this._run()},rerun:function(B,A){return this._run({action:"rerun",target_dataset_id:B.id,regions:A})},get_inputs_dict:function(){var A={};this.get("inputs").each(function(B){A[B.get("name")]=B.get("value")});return A},_run:function(C){var D=y.extend({tool_id:this.id,inputs:this.get_inputs_dict()},C);var B=$.Deferred(),A=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(D),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(E){return E!=="pending"}});$.when(A.go()).then(function(E){B.resolve(new z.DatasetCollection().reset(E))});return B}});y.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var w=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){y.each(this.attributes.elems,function(A){A.show()});this.show();this.set("open",false)},apply_search_results:function(B){var C=true,A;y.each(this.attributes.elems,function(D){if(D instanceof w){A=D;A.hide()}else{if(D instanceof j){if(D.apply_search_results(B)){C=false;if(A){A.show()}}}}});if(C){this.hide()}else{this.show();this.set("open",true)}}});y.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var C=this.attributes.query;if(C.length<this.attributes.min_chars_for_search){this.set("results",null);return}var B=C;if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var A=this;ga("send","pageview",galaxy_config.root+"?q="+B);this.timer=setTimeout(function(){$.get(A.attributes.search_url,{query:B},function(D){A.set("results",D);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},400)},clear_search:function(){this.set("query","");this.set("results",null)}});y.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(A){this.attributes.tool_search=A.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=A.tools;this.attributes.layout=new Backbone.Collection(this.parse(A.layout))},parse:function(B){var A=this,C=function(F){var E=F.model_class;if(E.indexOf("Tool")===E.length-4){return A.attributes.tools.get(F.id)}else{if(E==="ToolSection"){var D=y.map(F.elems,C);F.elems=D;return new l(F)}else{if(E==="ToolSectionLabel"){return new w(F)}}}};return y.map(B,C)},clear_search_results:function(){this.get("layout").each(function(A){if(A instanceof l){A.clear_search_results()}else{A.show()}})},apply_search_results:function(){var B=this.get("tool_search").get("results");if(B===null){this.clear_search_results();return}var A=null;this.get("layout").each(function(C){if(C instanceof w){A=C;A.hide()}else{if(C instanceof j){if(C.apply_search_results(B)){if(A){A.show()}}}else{A=null;C.apply_search_results(B)}}})}});var t=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=t.extend({tagName:"div",render:function(){var A=$("<div/>");A.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){A.find("a").on("click",function(B){B.preventDefault();Galaxy.upload.show()})}this.$el.append(A);return this}});var b=t.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=t.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){t.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var A=this.$el.find(".toolSectionBody");y.each(this.model.attributes.elems,function(B){if(B instanceof j){var C=new m({model:B,className:"toolTitle"});C.render();A.append(C.$el)}else{if(B instanceof w){var D=new b({model:B});D.render();A.append(D.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(A){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===A.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var x=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var A=this;var B=new p({model:this.model.get("tool_search")});B.render();A.$el.append(B.$el);this.model.get("layout").each(function(D){if(D instanceof l){var C=new r({model:D});C.render();A.$el.append(C.$el)}else{if(D instanceof j){var E=new m({model:D,className:"toolTitleNoSection"});E.render();A.$el.append(E.$el)}else{if(D instanceof w){var F=new b({model:D});F.render();A.$el.append(F.$el)}}}});A.$el.find("a.tool-link").click(function(E){var D=$(this).attr("class").split(/\s+/)[0],C=A.model.get("tools").get(D);A.trigger("tool_link_click",E,C)});return this},handle_search_results:function(){var A=this.model.get("tool_search").get("results");if(A&&A.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var v=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new x({collection:this.collection});this.tool_form_view=new v()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var A=this;this.tool_panel_view.on("tool_link_click",function(C,B){C.preventDefault();A.show_tool(B)})},show_tool:function(B){var A=this;B.fetch().done(function(){A.tool_form_view.model=B;A.tool_form_view.render();A.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:u,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:x,ToolFormView:v}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/6f09ebd33874/
Changeset: 6f09ebd33874
User: martenson
Date: 2015-03-02 22:19:11+00:00
Summary: compile handlebar templates
I wanted only one but the compilation alg probably changed so
am adding all
Affected #: 4 files
diff -r 14f402d4a6830e984a58bf626be2f8c40ae91b5a -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 static/scripts/templates/compiled/panel_section.js
--- a/static/scripts/templates/compiled/panel_section.js
+++ b/static/scripts/templates/compiled/panel_section.js
@@ -1,13 +1,14 @@
(function() {
var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
templates['panel_section'] = template({"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) {
- var helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression;
+ var helper, alias1=helpers.helperMissing, alias2="function", alias3=this.escapeExpression;
+
return "<div class=\"toolSectionTitle\" id=\"title_"
- + escapeExpression(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"id","hash":{},"data":data}) : helper)))
+ + alias3(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"id","hash":{},"data":data}) : helper)))
+ "\">\n <a href=\"javascript:void(0)\"><span>"
- + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper)))
+ + alias3(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"name","hash":{},"data":data}) : helper)))
+ "</span></a>\n</div>\n<div id=\""
- + escapeExpression(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"id","hash":{},"data":data}) : helper)))
+ + alias3(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"id","hash":{},"data":data}) : helper)))
+ "\" class=\"toolSectionBody\" style=\"display: none; \">\n <div class=\"toolSectionBg\"></div>\n<div>";
},"useData":true});
})();
\ No newline at end of file
diff -r 14f402d4a6830e984a58bf626be2f8c40ae91b5a -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 static/scripts/templates/compiled/tool_form.js
--- a/static/scripts/templates/compiled/tool_form.js
+++ b/static/scripts/templates/compiled/tool_form.js
@@ -1,26 +1,28 @@
(function() {
var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
templates['tool_form'] = template({"1":function(depth0,helpers,partials,data) {
- var stack1, helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression, buffer = " <div class=\"form-row\">\n <label for=\""
- + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper)))
+ var stack1, helper, alias1=helpers.helperMissing, alias2="function", alias3=this.escapeExpression;
+
+ return " <div class=\"form-row\">\n <label for=\""
+ + alias3(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"name","hash":{},"data":data}) : helper)))
+ "\">"
- + escapeExpression(((helper = (helper = helpers.label || (depth0 != null ? depth0.label : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"label","hash":{},"data":data}) : helper)))
- + ":</label>\n <div class=\"form-row-input\">\n ";
- stack1 = ((helper = (helper = helpers.html || (depth0 != null ? depth0.html : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"html","hash":{},"data":data}) : helper));
- if (stack1 != null) { buffer += stack1; }
- return buffer + "\n </div>\n <div class=\"toolParamHelp\" style=\"clear: both;\">\n "
- + escapeExpression(((helper = (helper = helpers.help || (depth0 != null ? depth0.help : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"help","hash":{},"data":data}) : helper)))
+ + alias3(((helper = (helper = helpers.label || (depth0 != null ? depth0.label : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"label","hash":{},"data":data}) : helper)))
+ + ":</label>\n <div class=\"form-row-input\">\n "
+ + ((stack1 = ((helper = (helper = helpers.html || (depth0 != null ? depth0.html : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"html","hash":{},"data":data}) : helper))) != null ? stack1 : "")
+ + "\n </div>\n <div class=\"toolParamHelp\" style=\"clear: both;\">\n "
+ + alias3(((helper = (helper = helpers.help || (depth0 != null ? depth0.help : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"help","hash":{},"data":data}) : helper)))
+ "\n </div>\n <div style=\"clear: both;\"></div>\n </div>\n";
},"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) {
- var stack1, helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression, buffer = "<div class=\"toolFormTitle\">"
- + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper)))
+ var stack1, helper, alias1=helpers.helperMissing, alias2="function", alias3=this.escapeExpression;
+
+ return "<div class=\"toolFormTitle\">"
+ + alias3(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"name","hash":{},"data":data}) : helper)))
+ " (version "
- + escapeExpression(((helper = (helper = helpers.version || (depth0 != null ? depth0.version : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"version","hash":{},"data":data}) : helper)))
- + ")</div>\n <div class=\"toolFormBody\">\n";
- stack1 = helpers.each.call(depth0, (depth0 != null ? depth0.inputs : depth0), {"name":"each","hash":{},"fn":this.program(1, data),"inverse":this.noop,"data":data});
- if (stack1 != null) { buffer += stack1; }
- return buffer + " </div>\n <div class=\"form-row form-actions\">\n <input type=\"submit\" class=\"btn btn-primary\" name=\"runtool_btn\" value=\"Execute\">\n</div>\n<div class=\"toolHelp\">\n <div class=\"toolHelpBody\">"
- + escapeExpression(((helper = (helper = helpers.help || (depth0 != null ? depth0.help : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"help","hash":{},"data":data}) : helper)))
+ + alias3(((helper = (helper = helpers.version || (depth0 != null ? depth0.version : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"version","hash":{},"data":data}) : helper)))
+ + ")</div>\n <div class=\"toolFormBody\">\n"
+ + ((stack1 = helpers.each.call(depth0,(depth0 != null ? depth0.inputs : depth0),{"name":"each","hash":{},"fn":this.program(1, data, 0),"inverse":this.noop,"data":data})) != null ? stack1 : "")
+ + " </div>\n <div class=\"form-row form-actions\">\n <input type=\"submit\" class=\"btn btn-primary\" name=\"runtool_btn\" value=\"Execute\">\n</div>\n<div class=\"toolHelp\">\n <div class=\"toolHelpBody\">"
+ + alias3(((helper = (helper = helpers.help || (depth0 != null ? depth0.help : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"help","hash":{},"data":data}) : helper)))
+ "</div>\n</div>";
},"useData":true});
})();
\ No newline at end of file
diff -r 14f402d4a6830e984a58bf626be2f8c40ae91b5a -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 static/scripts/templates/compiled/tool_link.js
--- a/static/scripts/templates/compiled/tool_link.js
+++ b/static/scripts/templates/compiled/tool_link.js
@@ -1,18 +1,19 @@
(function() {
var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
templates['tool_link'] = template({"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) {
- var helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression;
+ var helper, alias1=helpers.helperMissing, alias2="function", alias3=this.escapeExpression;
+
return "<a class=\""
- + escapeExpression(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"id","hash":{},"data":data}) : helper)))
+ + alias3(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"id","hash":{},"data":data}) : helper)))
+ " tool-link\" href=\""
- + escapeExpression(((helper = (helper = helpers.link || (depth0 != null ? depth0.link : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"link","hash":{},"data":data}) : helper)))
+ + alias3(((helper = (helper = helpers.link || (depth0 != null ? depth0.link : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"link","hash":{},"data":data}) : helper)))
+ "\" target=\""
- + escapeExpression(((helper = (helper = helpers.target || (depth0 != null ? depth0.target : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"target","hash":{},"data":data}) : helper)))
+ + alias3(((helper = (helper = helpers.target || (depth0 != null ? depth0.target : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"target","hash":{},"data":data}) : helper)))
+ "\" minsizehint=\""
- + escapeExpression(((helper = (helper = helpers.min_width || (depth0 != null ? depth0.min_width : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"min_width","hash":{},"data":data}) : helper)))
+ + alias3(((helper = (helper = helpers.min_width || (depth0 != null ? depth0.min_width : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"min_width","hash":{},"data":data}) : helper)))
+ "\">"
- + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper)))
+ + alias3(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"name","hash":{},"data":data}) : helper)))
+ "</a> "
- + escapeExpression(((helper = (helper = helpers.description || (depth0 != null ? depth0.description : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"description","hash":{},"data":data}) : helper)));
+ + alias3(((helper = (helper = helpers.description || (depth0 != null ? depth0.description : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"description","hash":{},"data":data}) : helper)));
},"useData":true});
})();
\ No newline at end of file
diff -r 14f402d4a6830e984a58bf626be2f8c40ae91b5a -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 static/scripts/templates/compiled/tool_search.js
--- a/static/scripts/templates/compiled/tool_search.js
+++ b/static/scripts/templates/compiled/tool_search.js
@@ -1,11 +1,12 @@
(function() {
var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
templates['tool_search'] = template({"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) {
- var helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression;
- return "<input type=\"text\" name=\"query\" value=\""
- + escapeExpression(((helper = (helper = helpers.search_hint_string || (depth0 != null ? depth0.search_hint_string : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"search_hint_string","hash":{},"data":data}) : helper)))
+ var helper, alias1=helpers.helperMissing, alias2="function", alias3=this.escapeExpression;
+
+ return "<input type=\"text\" name=\"query\" placeholder=\""
+ + alias3(((helper = (helper = helpers.search_hint_string || (depth0 != null ? depth0.search_hint_string : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"search_hint_string","hash":{},"data":data}) : helper)))
+ "\" id=\"tool-search-query\" autocomplete=\"off\" class=\"search-query parent-width\" />\n<a id=\"search-clear-btn\" title=\"clear search (esc)\"></a>\n<img src=\""
- + escapeExpression(((helper = (helper = helpers.spinner_url || (depth0 != null ? depth0.spinner_url : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"spinner_url","hash":{},"data":data}) : helper)))
- + "\" id=\"search-spinner\" class=\"search-spinner\"/>";
+ + alias3(((helper = (helper = helpers.spinner_url || (depth0 != null ? depth0.spinner_url : depth0)) != null ? helper : alias1),(typeof helper === alias2 ? helper.call(depth0,{"name":"spinner_url","hash":{},"data":data}) : helper)))
+ + "\" id=\"search-spinner\" class=\"search-spinner\"/>\n";
},"useData":true});
})();
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/a4f9af6ab587/
Changeset: a4f9af6ab587
User: dannon
Date: 2015-03-02 22:26:11+00:00
Summary: Change auth_debug behavior -- simply use an appropriate loglevel
Affected #: 10 files
diff -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 -r a4f9af6ab5870618d0318fca1d0af6b762f278bc config/galaxy.ini.sample
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -848,8 +848,6 @@
# (e.g. Active Directory) instead or in addition to local authentication
# (.sample is used if default does not exist).
#auth_config_file = config/auth_conf.xml
-# Print debugging info for auth
-#auth_debug = False
# Optional list of email addresses of API users who can make calls on behalf of
# other users.
diff -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 -r a4f9af6ab5870618d0318fca1d0af6b762f278bc lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -48,7 +48,6 @@
self.__plugins_dict = plugin_config.plugins_dict( galaxy.auth.providers, 'plugin_type' )
auth_config_file = app.config.auth_config_file
self.__init_authenticators(auth_config_file)
- self.debug = getattr(app.config, 'auth_debug', False)
def __init_authenticators(self, auth_config_file):
# parse XML
@@ -104,17 +103,16 @@
break
return message, status
- def check_auto_registration(self, trans, email, password, debug=False):
+ def check_auto_registration(self, trans, email, password):
"""
Checks the email/password using auth providers in order. If a match is
found, returns the 'auto-register' option for that provider.
"""
for provider, options in self.active_authenticators(email, password):
if provider is None:
- if debug:
- log.debug( "Unable to find module: %s" % options )
+ log.debug( "Unable to find module: %s" % options )
else:
- auth_result, auto_username = provider.authenticate(email, password, options, debug)
+ auth_result, auto_username = provider.authenticate(email, password, options)
auto_username = str(auto_username).lower()
if auth_result is True:
# make username unique
@@ -127,8 +125,7 @@
i += 1
else:
break # end for loop if we can't make a unique username
- if debug:
- log.debug( "Email: %s, auto-register with username: %s" % (email, auto_username) )
+ log.debug( "Email: %s, auto-register with username: %s" % (email, auto_username) )
return (_get_bool(options, 'auto-register', False), auto_username)
elif auth_result is None:
log.debug( "Email: %s, stopping due to failed non-continue" % (email) )
@@ -139,8 +136,7 @@
"""Checks the email/password using auth providers."""
for provider, options in self.active_authenticators(user.email, password):
if provider is None:
- if self.debug:
- log.debug( "Unable to find module: %s" % options )
+ log.debug( "Unable to find module: %s" % options )
else:
auth_result = provider.authenticate_user(user, password, options)
if auth_result is True:
@@ -155,8 +151,7 @@
"""
for provider, options in self.active_authenticators(user.email, current_password):
if provider is None:
- if self.debug:
- log.debug( "Unable to find module: %s" % options )
+ log.debug( "Unable to find module: %s" % options )
else:
if _get_bool(options, "allow-password-change", False):
auth_result = provider.authenticate_user(user, current_password, options)
@@ -182,8 +177,7 @@
continue # skip to next
yield authenticator.plugin, authenticator.options
except Exception:
- if self.debug:
- log.debug( ('Auth: Exception:\n%s' % (traceback.format_exc(),)) )
+ log.debug( ('Auth: Exception:\n%s' % (traceback.format_exc(),)) )
raise
Authenticator = namedtuple('Authenticator', ['plugin', 'filter_template', 'options'])
diff -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 -r a4f9af6ab5870618d0318fca1d0af6b762f278bc lib/galaxy/auth/providers/__init__.py
--- a/lib/galaxy/auth/providers/__init__.py
+++ b/lib/galaxy/auth/providers/__init__.py
@@ -16,7 +16,7 @@
""" Short string providing labelling this plugin """
@abc.abstractmethod
- def authenticate(self, username, password, options, debug=False):
+ def authenticate(self, username, password, options):
"""
Check that the username and password are correct.
@@ -29,8 +29,6 @@
:type password: str
:param options: options provided in auth_config_file
:type options: dict
- :param debug: whether to print debugging info (defaults to False)
- :type debug: bool
:returns: True: accept user, False: reject user and None: reject user
and don't try any other providers. str is the username to register
with if accepting
@@ -38,7 +36,7 @@
"""
@abc.abstractmethod
- def authenticate_user(self, user, password, options, debug=False):
+ def authenticate_user(self, user, password, options):
"""
Same as authenticate() method, except an User object is provided instead
of a username.
@@ -52,8 +50,6 @@
:type password: str
:param options: options provided in auth_config_file
:type options: dict
- :param debug: whether to print debugging info (defaults to False)
- :type debug: bool
:returns: True: accept user, False: reject user and None: reject user
and don't try any other providers
:rtype: bool
diff -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 -r a4f9af6ab5870618d0318fca1d0af6b762f278bc lib/galaxy/auth/providers/activedirectory.py
--- a/lib/galaxy/auth/providers/activedirectory.py
+++ b/lib/galaxy/auth/providers/activedirectory.py
@@ -27,13 +27,12 @@
"""
plugin_type = 'activedirectory'
- def authenticate(self, username, password, options, debug=False):
+ def authenticate(self, username, password, options):
"""
See abstract method documentation.
"""
- if debug:
- log.debug("Username: %s" % username)
- log.debug("Options: %s" % options)
+ log.debug("Username: %s" % username)
+ log.debug("Options: %s" % options)
failure_mode = False # reject but continue
if options.get('continue-on-failure', 'False') == 'False':
@@ -42,8 +41,7 @@
try:
import ldap
except:
- if debug:
- log.debug("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
+ log.debug("User: %s, ACTIVEDIRECTORY: False (no ldap)" % (username))
return (failure_mode, '')
# do AD search (if required)
@@ -64,8 +62,7 @@
# parse results
_, suser = l.result(result, 60)
_, attrs = suser[0]
- if debug:
- log.debug(("AD Search attributes: %s" % attrs))
+ log.debug(("AD Search attributes: %s" % attrs))
if hasattr(attrs, 'has_key'):
for attr in attributes:
if attr in attrs:
@@ -73,8 +70,7 @@
else:
vars[attr] = ""
except Exception:
- if debug:
- log.debug('User: %s, ACTIVEDIRECTORY: Search Exception:\n%s' % (username, traceback.format_exc(),))
+ log.debug('User: %s, ACTIVEDIRECTORY: Search Exception:\n%s' % (username, traceback.format_exc(),))
return (failure_mode, '')
# end search
@@ -86,19 +82,17 @@
l.protocol_version = 3
l.simple_bind_s(_get_subs(options, 'bind-user', vars), _get_subs(options, 'bind-password', vars))
except Exception:
- if debug:
- log.debug('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc()))
+ log.debug('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc()))
return (failure_mode, '')
- if debug:
- log.debug("User: %s, ACTIVEDIRECTORY: True" % (username))
+ log.debug("User: %s, ACTIVEDIRECTORY: True" % (username))
return (True, _get_subs(options, 'auto-register-username', vars))
- def authenticate_user(self, user, password, options, debug=False):
+ def authenticate_user(self, user, password, options):
"""
See abstract method documentation.
"""
- return self.authenticate(user.email, password, options, debug)[0]
+ return self.authenticate(user.email, password, options)[0]
__all__ = ['ActiveDirectory']
diff -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 -r a4f9af6ab5870618d0318fca1d0af6b762f278bc lib/galaxy/auth/providers/alwaysreject.py
--- a/lib/galaxy/auth/providers/alwaysreject.py
+++ b/lib/galaxy/auth/providers/alwaysreject.py
@@ -16,18 +16,17 @@
"""
plugin_type = 'alwaysreject'
- def authenticate(self, username, password, options, debug=False):
+ def authenticate(self, username, password, options):
"""
See abstract method documentation.
"""
return (None, '')
- def authenticate_user(self, user, password, options, debug=False):
+ def authenticate_user(self, user, password, options):
"""
See abstract method documentation.
"""
- if debug:
- log.debug("User: %s, ALWAYSREJECT: None" % (user.email))
+ log.debug("User: %s, ALWAYSREJECT: None" % (user.email))
return None
diff -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 -r a4f9af6ab5870618d0318fca1d0af6b762f278bc lib/galaxy/auth/providers/localdb.py
--- a/lib/galaxy/auth/providers/localdb.py
+++ b/lib/galaxy/auth/providers/localdb.py
@@ -13,19 +13,18 @@
"""Authenticate users against the local Galaxy database (as per usual)."""
plugin_type = 'localdb'
- def authenticate(self, username, password, options, debug=False):
+ def authenticate(self, username, password, options):
"""
See abstract method documentation.
"""
return (False, '') # it can never auto-create based of localdb (chicken-egg)
- def authenticate_user(self, user, password, options, debug=False):
+ def authenticate_user(self, user, password, options):
"""
See abstract method documentation.
"""
user_ok = user.check_password(password)
- if debug:
- log.debug("User: %s, LOCALDB: %s" % (user.email, user_ok))
+ log.debug("User: %s, LOCALDB: %s" % (user.email, user_ok))
return user_ok
diff -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 -r a4f9af6ab5870618d0318fca1d0af6b762f278bc lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -441,8 +441,6 @@
# Default chunk size for chunkable datatypes -- 64k
self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) )
- # auth
- self.auth_debug = string_as_bool( kwargs.get( 'auth_debug', False ) )
self.citation_cache_type = kwargs.get( "citation_cache_type", "file" )
self.citation_cache_data_dir = self.resolve_path( kwargs.get( "citation_cache_data_dir", "database/citations/data" ) )
diff -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 -r a4f9af6ab5870618d0318fca1d0af6b762f278bc lib/galaxy/webapps/galaxy/controllers/mobile.py
--- a/lib/galaxy/webapps/galaxy/controllers/mobile.py
+++ b/lib/galaxy/webapps/galaxy/controllers/mobile.py
@@ -58,7 +58,7 @@
# error = password_error = None
# user = trans.sa_session.query( model.User ).filter_by( email = email ).first()
# if not user:
- # autoreg = galaxy.auth.check_auto_registration(trans, email, password, trans.app.config.auth_config_file, trans.app.config.auth_debug)
+ # autoreg = galaxy.auth.check_auto_registration(trans, email, password, trans.app.config.auth_config_file)
# if autoreg[0]:
# kwd = {}
# kwd['username'] = autoreg[1]
@@ -82,7 +82,7 @@
# error = "This account has been marked deleted, contact your Galaxy administrator to restore the account."
# elif user.external:
# error = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it."
- # elif not galaxy.auth.check_password(user, password, trans.app.config.auth_config_file, trans.app.config.auth_debug):
+ # elif not galaxy.auth.check_password(user, password, trans.app.config.auth_config_file):
# error = "Invalid password"
# else:
# trans.handle_user_login( user )
diff -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 -r a4f9af6ab5870618d0318fca1d0af6b762f278bc lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -514,9 +514,7 @@
redirect = kwd.get( 'redirect', trans.request.referer ).strip()
success = False
user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first()
- if trans.app.config.auth_debug:
- print ("trans.app.config.auth_config_file: %s" % trans.app.config.auth_config_file)
- print ("trans.app.config.auth_debug: %s WARNING: don't use in production" % trans.app.config.auth_debug)
+ log.debug("trans.app.config.auth_config_file: %s" % trans.app.config.auth_config_file)
if not user:
autoreg = trans.app.auth_manager.check_auto_registration(trans, email, password)
if autoreg[0]:
diff -r 6f09ebd33874856a2495fedeeb5e85e2c6203362 -r a4f9af6ab5870618d0318fca1d0af6b762f278bc lib/galaxy/webapps/tool_shed/config.py
--- a/lib/galaxy/webapps/tool_shed/config.py
+++ b/lib/galaxy/webapps/tool_shed/config.py
@@ -132,7 +132,6 @@
if global_conf and "__file__" in global_conf:
global_conf_parser.read(global_conf['__file__'])
self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) )
- self.auth_debug = string_as_bool( kwargs.get( 'auth_debug', False ) )
self.citation_cache_type = kwargs.get( "citation_cache_type", "file" )
self.citation_cache_data_dir = resolve_path( kwargs.get( "citation_cache_data_dir", "database/tool_shed_citations/data" ), self.root )
self.citation_cache_lock_dir = resolve_path( kwargs.get( "citation_cache_lock_dir", "database/tool_shed_citations/locks" ), self.root )
https://bitbucket.org/galaxy/galaxy-central/commits/13ff916e7fc0/
Changeset: 13ff916e7fc0
User: dannon
Date: 2015-03-02 22:35:14+00:00
Summary: Swap logging in auth exception handling to use log.exception
Affected #: 2 files
diff -r a4f9af6ab5870618d0318fca1d0af6b762f278bc -r 13ff916e7fc049900a1233e84e9a140c8491de36 lib/galaxy/auth/__init__.py
--- a/lib/galaxy/auth/__init__.py
+++ b/lib/galaxy/auth/__init__.py
@@ -3,7 +3,6 @@
"""
from collections import namedtuple
-import traceback
import xml.etree.ElementTree
from galaxy.security.validate_user_input import validate_publicname
@@ -177,7 +176,7 @@
continue # skip to next
yield authenticator.plugin, authenticator.options
except Exception:
- log.debug( ('Auth: Exception:\n%s' % (traceback.format_exc(),)) )
+ log.exception( "Active Authenticators Failure" )
raise
Authenticator = namedtuple('Authenticator', ['plugin', 'filter_template', 'options'])
diff -r a4f9af6ab5870618d0318fca1d0af6b762f278bc -r 13ff916e7fc049900a1233e84e9a140c8491de36 lib/galaxy/auth/providers/activedirectory.py
--- a/lib/galaxy/auth/providers/activedirectory.py
+++ b/lib/galaxy/auth/providers/activedirectory.py
@@ -4,7 +4,6 @@
@author: Andrew Robinson
"""
-import traceback
from ..providers import AuthProvider
import logging
@@ -70,7 +69,7 @@
else:
vars[attr] = ""
except Exception:
- log.debug('User: %s, ACTIVEDIRECTORY: Search Exception:\n%s' % (username, traceback.format_exc(),))
+ log.exception('ACTIVEDIRECTORY Search Exception for User: %s' % username)
return (failure_mode, '')
# end search
@@ -82,7 +81,7 @@
l.protocol_version = 3
l.simple_bind_s(_get_subs(options, 'bind-user', vars), _get_subs(options, 'bind-password', vars))
except Exception:
- log.debug('User: %s, ACTIVEDIRECTORY: Authenticate Exception:\n%s' % (username, traceback.format_exc()))
+ log.exception('ACTIVEDIRECTORY Authenticate Exception for User %s' % username)
return (failure_mode, '')
log.debug("User: %s, ACTIVEDIRECTORY: True" % (username))
https://bitbucket.org/galaxy/galaxy-central/commits/614be0554e42/
Changeset: 614be0554e42
User: dannon
Date: 2015-03-03 00:51:46+00:00
Summary: Fix bug in toolshed set_tool_versions during error case
Affected #: 1 file
diff -r 13ff916e7fc049900a1233e84e9a140c8491de36 -r 614be0554e42399b32dbfc5982bd72f9f98137a5 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1763,9 +1763,9 @@
message = "Tool versions have been set for all included tools."
status = 'done'
else:
- message = "Version information for the tools included in the <b>%s</b> repository is missing. " % escape( repository.name )
- message += "Reset all of this reppository's metadata in the tool shed, then set the installed tool versions "
- message ++ "from the installed repository's <b>Repository Actions</b> menu. "
+ message = ("Version information for the tools included in the <b>%s</b> repository is missing. "
+ "Reset all of this reppository's metadata in the tool shed, then set the installed tool versions "
+ "from the installed repository's <b>Repository Actions</b> menu. " % escape( repository.name ))
status = 'error'
shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository )
repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) )
https://bitbucket.org/galaxy/galaxy-central/commits/c0321a70f8f5/
Changeset: c0321a70f8f5
User: dannon
Date: 2015-03-03 01:10:28+00:00
Summary: Fix another bug in admin_toolshed controller encountered if tool_dependency_dir not set but deps are defined
Affected #: 1 file
diff -r 614be0554e42399b32dbfc5982bd72f9f98137a5 -r c0321a70f8f58e06859453e834d273cac4509ef7 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -614,10 +614,10 @@
self.initiate_tool_dependency_installation( trans, tool_dependencies, message=message, status=status )
# Handle tool dependencies check box.
if trans.app.config.tool_dependency_dir is None:
- if includes_tool_dependencies:
- message = "Tool dependencies defined in this repository can be automatically installed if you set "
- message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file "
- message += "(galaxy.ini) and restart your Galaxy server."
+ if tool_dependencies_dict:
+ message = ("Tool dependencies defined in this repository can be automatically installed if you set "
+ "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file "
+ "(galaxy.ini) and restart your Galaxy server.")
status = "warning"
install_tool_dependencies_check_box_checked = False
else:
https://bitbucket.org/galaxy/galaxy-central/commits/8af2b8d5c8cd/
Changeset: 8af2b8d5c8cd
User: dannon
Date: 2015-03-03 01:43:37+00:00
Summary: Remove cruft and unused vars, cleanup/pep8 in admin_toolshed controller.
Affected #: 1 file
diff -r c0321a70f8f58e06859453e834d273cac4509ef7 -r 8af2b8d5c8cd1ab84021a7e1197b7d38d946b62f lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -199,7 +199,6 @@
@web.require_admin
def browse_tool_sheds( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
- status = kwd.get( 'status', 'done' )
return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako',
message=message,
status='error' )
@@ -216,8 +215,7 @@
str( repository.name ),
str( repository.owner ),
str( repository.changeset_revision ) )
- url = common_util.url_join( tool_shed_url,
- 'repository/check_for_updates%s' % params )
+ url = common_util.url_join( tool_shed_url, 'repository/check_for_updates%s' % params )
return trans.response.send_redirect( url )
@web.expose
@@ -331,7 +329,7 @@
image can be defined in either a README.rst file contained in the repository or the help section of a Galaxy tool config that
is contained in the repository. The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer
required, and is now ignored.
- .. image:: https://raw.github.com/galaxy/some_image.png
+ .. image:: https://raw.github.com/galaxy/some_image.png
.. image:: $PATH_TO_IMAGES/some_image.png
.. image:: /static/images/some_image.gif
.. image:: some_image.jpg
@@ -348,7 +346,7 @@
file_name = os.path.basename( relative_path_to_image_file )
try:
extension = file_name.split( '.' )[ -1 ]
- except Exception, e:
+ except Exception:
extension = None
if extension:
mimetype = trans.app.datatypes_registry.get_mimetype_by_extension( extension )
@@ -497,7 +495,6 @@
text = util.unicodify( installed_tool_dependency.error_message )
if text is not None:
err_msg += ' %s' % text
- tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies ]
if err_msg:
message += err_msg
status = 'error'
@@ -604,7 +601,7 @@
updated_metadata_dict=updated_metadata,
updated_changeset_revision=updating_to_changeset_revision,
updated_ctx_rev=updating_to_ctx_rev )
- if install_tool_dependencies:
+ if includes_tool_dependencies:
tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app,
repository,
relative_install_dir,
@@ -641,7 +638,6 @@
@web.require_admin
def manage_repositories( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
- status = kwd.get( 'status', 'done' )
tsridslist = common_util.get_tool_shed_repository_ids( **kwd )
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
@@ -857,7 +853,7 @@
# The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a
# tool dependency, but they didn't check any of the available tool dependencies on which to perform the action.
tool_shed_repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
- self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies" % escape( tool_shed_repository.name )
+ self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies" % escape( tool_shed_repository.name )
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
if not tool_dependency_ids:
@@ -1018,12 +1014,9 @@
repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ]
dd = dependency_display.DependencyDisplayer( trans.app )
install_repository_manager = install_manager.InstallRepositoryManager( trans.app )
- if ( not includes_tools_for_display_in_tool_panel and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or \
- ( includes_tools_for_display_in_tool_panel and kwd.get( 'select_tool_panel_section_button', False ) ):
+ if ( ( not includes_tools_for_display_in_tool_panel and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or
+ ( includes_tools_for_display_in_tool_panel and kwd.get( 'select_tool_panel_section_button', False ) ) ):
if updating:
- encoded_updated_metadata_dict = kwd.get( 'encoded_updated_metadata_dict', None )
- updated_changeset_revision = kwd.get( 'updated_changeset_revision', None )
- updated_ctx_rev = kwd.get( 'updated_ctx_rev', None )
repository = suc.get_tool_shed_repository_by_id( trans.app, updating_repository_id )
decoded_updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata )
# Now that the user has decided whether they will handle dependencies, we can update
@@ -1090,7 +1083,6 @@
repo_info_dict,
includes_tool_dependencies,
updating=updating )
- changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None )
if not has_repository_dependencies:
has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False )
if not includes_tool_dependencies:
@@ -1104,8 +1096,6 @@
installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None )
missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None )
missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None )
- name = dependencies_for_repository_dict.get( 'name', None )
- repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None )
readme_files_dict = readme_util.get_readme_files_dict_for_display( trans.app, tool_shed_url, repo_info_dict )
# We're handling 1 of 3 scenarios here: (1) we're installing a tool shed repository for the first time, so we've
# retrieved the list of installed and missing repository dependencies from the database (2) we're handling the
@@ -1128,14 +1118,12 @@
else:
# We're installing a list of repositories, each of which may have tool dependencies or repository dependencies.
containers_dicts = []
- installed_repository_manager = trans.app.installed_repository_manager
for repo_info_dict in repo_info_dicts:
dependencies_for_repository_dict = \
trans.app.installed_repository_manager.get_dependencies_for_repository( tool_shed_url,
repo_info_dict,
includes_tool_dependencies,
updating=updating )
- changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None )
if not has_repository_dependencies:
has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False )
if not includes_tool_dependencies:
@@ -1149,17 +1137,16 @@
installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None )
missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None )
missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None )
- name = dependencies_for_repository_dict.get( 'name', None )
- repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None )
- containers_dict = \
- dd.populate_containers_dict_for_new_install( tool_shed_url=tool_shed_url,
- tool_path=tool_path,
- readme_files_dict=None,
- installed_repository_dependencies=installed_repository_dependencies,
- missing_repository_dependencies=missing_repository_dependencies,
- installed_tool_dependencies=installed_tool_dependencies,
- missing_tool_dependencies=missing_tool_dependencies,
- updating=updating )
+ containers_dict = dd.populate_containers_dict_for_new_install(
+ tool_shed_url=tool_shed_url,
+ tool_path=tool_path,
+ readme_files_dict=None,
+ installed_repository_dependencies=installed_repository_dependencies,
+ missing_repository_dependencies=missing_repository_dependencies,
+ installed_tool_dependencies=installed_tool_dependencies,
+ missing_tool_dependencies=missing_tool_dependencies,
+ updating=updating
+ )
containers_dicts.append( containers_dict )
# Merge all containers into a single container.
containers_dict = dd.merge_containers_dicts_for_new_install( containers_dicts )
@@ -1280,10 +1267,6 @@
shed_tool_conf, tool_path, relative_install_dir = \
suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository )
repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository )
- clone_dir = os.path.join( tool_path,
- suc.generate_tool_shed_repository_install_dir( repository_clone_url,
- tool_shed_repository.installed_changeset_revision ) )
- relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name )
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_repository.tool_shed )
tool_section = None
tool_panel_section_id = kwd.get( 'tool_panel_section_id', '' )
@@ -1381,7 +1364,7 @@
tool_shed_repository_ids=encoded_repository_ids,
tool_shed_url=tool_shed_url )
encoded_kwd = encoding_util.tool_shed_encode( new_kwd )
- tsr_ids = [ r.id for r in created_or_updated_tool_shed_repositories ]
+ tsr_ids = [ r.id for r in created_or_updated_tool_shed_repositories ]
tool_shed_repositories = []
for tsr_id in tsr_ids:
tsr = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( tsr_id )
@@ -1452,8 +1435,8 @@
# The received lists of tool_shed_repositories and repo_info_dicts are ordered.
for index, tool_shed_repository in enumerate( tool_shed_repositories ):
repo_info_dict = repo_info_dicts[ index ]
- repair_dict = repair_repository_manager.repair_tool_shed_repository( tool_shed_repository,
- encoding_util.tool_shed_encode( repo_info_dict ) )
+ repair_repository_manager.repair_tool_shed_repository( tool_shed_repository,
+ encoding_util.tool_shed_encode( repo_info_dict ) )
tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ]
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
action='monitor_repository_installation',
@@ -1477,7 +1460,7 @@
status=repository.status,
html_status=unicode( trans.fill_template( "admin/tool_shed_repository/repository_installation_status.mako",
repository=repository ),
- 'utf-8' ) ) )
+ 'utf-8' ) ) )
return rval
@web.expose
@@ -1568,7 +1551,6 @@
repo_info_dict,
includes_tool_dependencies,
updating=False )
- changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None )
has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False )
includes_tool_dependencies = dependencies_for_repository_dict.get( 'includes_tool_dependencies', False )
includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False )
@@ -1577,8 +1559,6 @@
installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None )
missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None )
missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None )
- repository_name = dependencies_for_repository_dict.get( 'name', None )
- repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None )
if installed_repository_dependencies or missing_repository_dependencies:
has_repository_dependencies = True
else:
@@ -1691,7 +1671,7 @@
repository=repository,
changeset_revision=repository.changeset_revision,
repository_clone_url=repository_clone_url,
- shed_config_dict = repository.get_shed_config_dict( trans.app ),
+ shed_config_dict=repository.get_shed_config_dict( trans.app ),
relative_install_dir=relative_install_dir,
repository_files_dir=None,
resetting_all_metadata_on_repository=False,
@@ -1801,7 +1781,7 @@
status=tool_dependency.status,
html_status=unicode( trans.fill_template( "admin/tool_shed_repository/tool_dependency_installation_status.mako",
tool_dependency=tool_dependency ),
- 'utf-8' ) ) )
+ 'utf-8' ) ) )
return rval
@web.expose
@@ -1923,12 +1903,12 @@
# Add new Data Manager entries
if 'data_manager' in irmm_metadata_dict:
dmh = data_manager.DataManagerHandler( trans.app )
- new_data_managers = dmh.install_data_managers( trans.app.config.shed_data_manager_config_file,
- irmm_metadata_dict,
- repository.get_shed_config_dict( trans.app ),
- os.path.join( relative_install_dir, name ),
- repository,
- repository_tools_tups )
+ dmh.install_data_managers( trans.app.config.shed_data_manager_config_file,
+ irmm_metadata_dict,
+ repository.get_shed_config_dict( trans.app ),
+ os.path.join( relative_install_dir, name ),
+ repository,
+ repository_tools_tups )
if 'repository_dependencies' in irmm_metadata_dict or 'tool_dependencies' in irmm_metadata_dict:
new_repository_dependencies_dict = irmm_metadata_dict.get( 'repository_dependencies', {} )
new_repository_dependencies = new_repository_dependencies_dict.get( 'repository_dependencies', [] )
@@ -2000,7 +1980,7 @@
encoded_relative_install_dir=encoded_relative_install_dir,
encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
message=message,
- status = status )
+ status=status )
return self.install_tool_dependencies_with_update( trans, **new_kwd )
# Updates received did not include any newly defined repository dependencies or newly defined
# tool dependencies that need to be installed.
https://bitbucket.org/galaxy/galaxy-central/commits/13cc751d07ed/
Changeset: 13cc751d07ed
User: dannon
Date: 2015-03-03 01:51:40+00:00
Summary: One more bugfix in admin_toolshed / undefined var.
Affected #: 1 file
diff -r 8af2b8d5c8cd1ab84021a7e1197b7d38d946b62f -r 13cc751d07ed98a6c0ebbd781a8c6319a7f8e1f9 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -589,7 +589,6 @@
encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None )
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
- install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
if 'install_tool_dependencies_with_update_button' in kwd:
# Now that the user has chosen whether to install tool dependencies or not, we can
# update the repository record with the changes in the updated revision.
@@ -601,7 +600,7 @@
updated_metadata_dict=updated_metadata,
updated_changeset_revision=updating_to_changeset_revision,
updated_ctx_rev=updating_to_ctx_rev )
- if includes_tool_dependencies:
+ if tool_dependencies_dict:
tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app,
repository,
relative_install_dir,
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] f9e170: Add GXYcast1 slied to highlight new tools & Featur...
by GitHub 28 Feb '15
by GitHub 28 Feb '15
28 Feb '15
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: f9e1704b38cbffacbfc02924436b9c717f7f8043
https://github.com/galaxyproject/usegalaxy-playbook/commit/f9e1704b38cbffac…
Author: Dave Clements <clements(a)Clements-Galaxy.local>
Date: 2015-02-28 (Sat, 28 Feb 2015)
Changed paths:
A files/galaxy/common/static/welcome_img/GalaxyCast1.png
M templates/galaxy/common/static/welcome.html.j2
Log Message:
-----------
Add GXYcast1 slied to highlight new tools & Features.
Dropped Screencasts are back slide.
1
0
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: b4dc38f009a2632db39382b9954ed14ec39ff34c
https://github.com/galaxyproject/usegalaxy-playbook/commit/b4dc38f009a2632d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-02-27 (Fri, 27 Feb 2015)
Changed paths:
M production/group_vars/all.yml
M stage/group_vars/all.yml
Log Message:
-----------
Update Test and Main
1
0
3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/edae5af34677/
Changeset: edae5af34677
Branch: release_15.03
User: dannon
Date: 2015-02-27 00:59:26+00:00
Summary: Fix server_starttime being in app for reports, toolshed. I will be refactoring this shortly to have a base UniverseApplication from which things inherit.
Affected #: 2 files
diff -r 12a2f45243502295e324bf6656481a98c61101c0 -r edae5af346776161c139666c33f15066f769cdb5 lib/galaxy/webapps/reports/app.py
--- a/lib/galaxy/webapps/reports/app.py
+++ b/lib/galaxy/webapps/reports/app.py
@@ -1,5 +1,7 @@
+import config
import sys
-import config
+import time
+
import galaxy.model
from galaxy.web import security
@@ -26,6 +28,8 @@
self.targets_mysql = 'mysql' in self.config.database_connection
# Security helper
self.security = security.SecurityHelper( id_secret=self.config.id_secret )
+ # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
+ self.server_starttime = int(time.time())
def shutdown( self ):
pass
diff -r 12a2f45243502295e324bf6656481a98c61101c0 -r edae5af346776161c139666c33f15066f769cdb5 lib/galaxy/webapps/tool_shed/app.py
--- a/lib/galaxy/webapps/tool_shed/app.py
+++ b/lib/galaxy/webapps/tool_shed/app.py
@@ -1,17 +1,18 @@
import config
import sys
+import time
+import galaxy.datatypes.registry
+import galaxy.quota
+import galaxy.tools.data
+import galaxy.webapps.tool_shed.model
from galaxy import tools
-import galaxy.tools.data
-import galaxy.quota
-import galaxy.datatypes.registry
-import galaxy.webapps.tool_shed.model
+from galaxy.managers.tags import CommunityTagManager
from galaxy.openid.providers import OpenIDProviders
from galaxy.util.dbkeys import GenomeBuilds
from galaxy.web import security
-from galaxy.managers.tags import CommunityTagManager
-from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
import tool_shed.repository_registry
import tool_shed.repository_types.registry
+from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
class UniverseApplication( object ):
@@ -70,6 +71,8 @@
self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
# Initialize the repository registry.
self.repository_registry = tool_shed.repository_registry.Registry( self )
+ # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
+ self.server_starttime = int(time.time())
print >> sys.stderr, "Tool shed hgweb.config file is: ", self.hgweb_config_manager.hgweb_config
def shutdown( self ):
https://bitbucket.org/galaxy/galaxy-central/commits/be0aa5c296c7/
Changeset: be0aa5c296c7
Branch: release_15.03
User: dan
Date: 2015-02-27 20:50:13+00:00
Summary: Allow External display applications to use Tool Data Tables.
Affected #: 7 files
diff -r edae5af346776161c139666c33f15066f769cdb5 -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -88,7 +88,7 @@
# Load proprietary datatype converters and display applications.
self.installed_repository_manager.load_proprietary_converters_and_display_applications()
# Load datatype display applications defined in local datatypes_conf.xml
- self.datatypes_registry.load_display_applications()
+ self.datatypes_registry.load_display_applications( self )
# Load datatype converters defined in local datatypes_conf.xml
self.datatypes_registry.load_datatype_converters( self.toolbox )
# Load external metadata tool
diff -r edae5af346776161c139666c33f15066f769cdb5 -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 lib/galaxy/datatypes/display_applications/application.py
--- a/lib/galaxy/datatypes/display_applications/application.py
+++ b/lib/galaxy/datatypes/display_applications/application.py
@@ -80,21 +80,57 @@
return True
class DynamicDisplayApplicationBuilder( object ):
- @classmethod
+
def __init__( self, elem, display_application, build_sites ):
- rval = []
filename = None
+ data_table = None
if elem.get( 'site_type', None ) is not None:
filename = build_sites.get( elem.get( 'site_type' ) )
else:
filename = elem.get( 'from_file', None )
- assert filename is not None, 'Filename and id attributes required for dynamic_links'
+ if filename is None:
+ data_table_name = elem.get( 'from_data_table', None )
+ if data_table_name:
+ data_table = display_application.app.tool_data_tables.get( data_table_name, None )
+ assert data_table is not None, 'Unable to find data table named "%s".' % data_table_name
+
+ assert filename is not None or data_table is not None,'Filename or data Table is required for dynamic_links.'
skip_startswith = elem.get( 'skip_startswith', None )
separator = elem.get( 'separator', '\t' )
- id_col = int( elem.get( 'id', None ) )
- name_col = int( elem.get( 'name', id_col ) )
+ id_col = elem.get( 'id', None )
+ try:
+ id_col = int( id_col )
+ except:
+ if data_table:
+ if id_col is None:
+ id_col = data_table.columns.get( 'id', None )
+ if id_col is None:
+ id_col = data_table.columns.get( 'value', None )
+ try:
+ id_col = int( id_col )
+ except:
+ # id is set to a string or None, use column by that name if available
+ id_col = data_table.columns.get( id_col, None )
+ id_col = int( id_col )
+ name_col = elem.get( 'name', None )
+ try:
+ name_col = int( name_col )
+ except:
+ if data_table:
+ if name_col is None:
+ name_col = data_table.columns.get( 'name', None )
+ else:
+ name_col = data_table.columns.get( name_col, None )
+ else:
+ name_col = None
+ if name_col is None:
+ name_col = id_col
+ max_col = max( id_col, name_col )
dynamic_params = {}
- max_col = max( id_col, name_col )
+ if data_table is not None:
+ max_col = max( [ max_col ] + data_table.columns.values() )
+ for key, value in data_table.columns.items():
+ dynamic_params[key] = { 'column': value, 'split': False, 'separator': ',' }
for dynamic_param in elem.findall( 'dynamic_param' ):
name = dynamic_param.get( 'name' )
value = int( dynamic_param.get( 'value' ) )
@@ -102,27 +138,38 @@
param_separator = dynamic_param.get( 'separator', ',' )
max_col = max( max_col, value )
dynamic_params[name] = { 'column': value, 'split': split, 'separator': param_separator }
- for line in open( filename ):
- if not skip_startswith or not line.startswith( skip_startswith ):
- line = line.rstrip( '\n\r' )
- if not line:
+ if filename:
+ data_iter = open( filename )
+ elif data_table:
+ version, data_iter = data_table.get_version_fields()
+ display_application.add_data_table_watch( data_table.name, version )
+ links = []
+ for line in data_iter:
+ if isinstance( line, basestring ):
+ if not skip_startswith or not line.startswith( skip_startswith ):
+ line = line.rstrip( '\n\r' )
+ if not line:
+ continue
+ fields = line.split( separator )
+ else:
continue
- fields = line.split( separator )
- if len( fields ) > max_col:
- new_elem = deepcopy( elem )
- new_elem.set( 'id', fields[id_col] )
- new_elem.set( 'name', fields[name_col] )
- dynamic_values = {}
- for key, attributes in dynamic_params.iteritems():
- value = fields[ attributes[ 'column' ] ]
- if attributes['split']:
- value = value.split( attributes['separator'] )
- dynamic_values[key] = value
- #now populate
- rval.append( DisplayApplicationLink.from_elem( new_elem, display_application, other_values = dynamic_values ) )
- else:
- log.warning( 'Invalid dynamic display application link specified in %s: "%s"' % ( filename, line ) )
- self.links = rval
+ else:
+ fields = line
+ if len( fields ) > max_col:
+ new_elem = deepcopy( elem )
+ new_elem.set( 'id', fields[id_col] )
+ new_elem.set( 'name', fields[name_col] )
+ dynamic_values = {}
+ for key, attributes in dynamic_params.iteritems():
+ value = fields[ attributes[ 'column' ] ]
+ if attributes['split']:
+ value = value.split( attributes['separator'] )
+ dynamic_values[key] = value
+ #now populate
+ links.append( DisplayApplicationLink.from_elem( new_elem, display_application, other_values = dynamic_values ) )
+ else:
+ log.warning( 'Invalid dynamic display application link specified in %s: "%s"' % ( filename, line ) )
+ self.links = links
def __iter__( self ):
return iter( self.links )
@@ -166,12 +213,12 @@
class DisplayApplication( object ):
@classmethod
- def from_file( cls, filename, datatypes_registry ):
- return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry, filename=filename )
+ def from_file( cls, filename, app ):
+ return cls.from_elem( parse_xml( filename ).getroot(), app, filename=filename )
@classmethod
- def from_elem( cls, elem, datatypes_registry, filename=None ):
+ def from_elem( cls, elem, app, filename=None ):
att_dict = cls._get_attributes_from_elem( elem )
- rval = DisplayApplication( att_dict['id'], att_dict['name'], datatypes_registry, att_dict['version'], filename=filename, elem=elem )
+ rval = DisplayApplication( att_dict['id'], att_dict['name'], app, att_dict['version'], filename=filename, elem=elem )
rval._load_links_from_elem( elem )
return rval
@classmethod
@@ -181,29 +228,32 @@
name = elem.get( 'name', display_id )
version = elem.get( 'version', None )
return dict( id=display_id, name=name, version=version )
- def __init__( self, display_id, name, datatypes_registry, version = None, filename=None, elem=None ):
+ def __init__( self, display_id, name, app, version = None, filename=None, elem=None ):
self.id = display_id
self.name = name
- self.datatypes_registry = datatypes_registry
+ self.app = app
if version is None:
version = "1.0.0"
self.version = version
self.links = odict()
self._filename = filename
self._elem = elem
+ self._data_table_versions = {}
def _load_links_from_elem( self, elem ):
for link_elem in elem.findall( 'link' ):
link = DisplayApplicationLink.from_elem( link_elem, self )
if link:
self.links[ link.id ] = link
for dynamic_links in elem.findall( 'dynamic_links' ):
- for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.datatypes_registry.build_sites ):
+ for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.app.datatypes_registry.build_sites ):
self.links[ link.id ] = link
def get_link( self, link_name, data, dataset_hash, user_hash, trans, app_kwds ):
#returns a link object with data knowledge to generate links
+ self._check_and_reload()
return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans, app_kwds )
def filter_by_dataset( self, data, trans ):
- filtered = DisplayApplication( self.id, self.name, self.datatypes_registry, version = self.version )
+ self._check_and_reload()
+ filtered = DisplayApplication( self.id, self.name, self.app, version = self.version )
for link_name, link_value in self.links.iteritems():
if link_value.filter_by_dataset( data, trans ):
filtered.links[link_name] = link_value
@@ -222,9 +272,24 @@
# clear old links
for key in self.links.keys():
del self.links[key]
+ #clear data table versions:
+ for key in self._data_table_versions.keys():
+ del self._data_table_versions[ key ]
# Set new attributes
for key, value in attr_dict.iteritems():
setattr( self, key, value )
# Load new links
self._load_links_from_elem( elem )
return self
+ def add_data_table_watch( self, table_name, version=None ):
+ self._data_table_versions[ table_name ] = version
+ def _requires_reload( self ):
+ for key, value in self._data_table_versions.iteritems():
+ table = self.app.tool_data_tables.get( key, None )
+ if table and not table.is_current_version( value ):
+ return True
+ return False
+ def _check_and_reload( self ):
+ if self._requires_reload():
+ self.reload()
+
diff -r edae5af346776161c139666c33f15066f769cdb5 -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 lib/galaxy/datatypes/display_applications/parameters.py
--- a/lib/galaxy/datatypes/display_applications/parameters.py
+++ b/lib/galaxy/datatypes/display_applications/parameters.py
@@ -59,7 +59,7 @@
@property
def formats( self ):
if self.extensions:
- return tuple( map( type, map( self.link.display_application.datatypes_registry.get_datatype_by_extension, self.extensions ) ) )
+ return tuple( map( type, map( self.link.display_application.app.datatypes_registry.get_datatype_by_extension, self.extensions ) ) )
return None
def _get_dataset_like_object( self, other_values ):
#this returned object has file_name, state, and states attributes equivalent to a DatasetAssociation
diff -r edae5af346776161c139666c33f15066f769cdb5 -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -546,7 +546,7 @@
else:
self.log.exception( "Error loading converter (%s): %s" % ( converter_path, str( e ) ) )
- def load_display_applications( self, installed_repository_dict=None, deactivate=False ):
+ def load_display_applications( self, app, installed_repository_dict=None, deactivate=False ):
"""
If deactivate is False, add display applications from self.display_app_containers or
self.proprietary_display_app_containers to appropriate datatypes. If deactivate is
@@ -570,7 +570,7 @@
config_path = os.path.join( self.display_applications_path, display_file )
try:
inherit = galaxy.util.string_as_bool( display_app.get( 'inherit', 'False' ) )
- display_app = DisplayApplication.from_file( config_path, self )
+ display_app = DisplayApplication.from_file( config_path, app )
if display_app:
if display_app.id in self.display_applications:
if deactivate:
diff -r edae5af346776161c139666c33f15066f769cdb5 -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
--- a/lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
+++ b/lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
@@ -214,5 +214,5 @@
def load_installed_display_applications( self, installed_repository_dict, deactivate=False ):
"""Load or deactivate custom datatype display applications."""
- self.app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict,
+ self.app.datatypes_registry.load_display_applications( self.app, installed_repository_dict=installed_repository_dict,
deactivate=deactivate )
diff -r edae5af346776161c139666c33f15066f769cdb5 -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -621,7 +621,7 @@
self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, installed_repository_dict=repository_dict )
if display_path:
# Load proprietary datatype display applications
- self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
+ self.app.datatypes_registry.load_display_applications( self.app, installed_repository_dict=repository_dict )
def handle_tool_shed_repositories( self, installation_dict, using_api=False ):
# The following installation_dict entries are all required.
diff -r edae5af346776161c139666c33f15066f769cdb5 -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 lib/tool_shed/galaxy_install/tool_migration_manager.py
--- a/lib/tool_shed/galaxy_install/tool_migration_manager.py
+++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py
@@ -523,7 +523,7 @@
installed_repository_dict=repository_dict )
if display_path:
# Load proprietary datatype display applications
- self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
+ self.app.datatypes_registry.load_display_applications( self.app, installed_repository_dict=repository_dict )
basic_util.remove_dir( work_dir )
def install_repository( self, repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=False ):
https://bitbucket.org/galaxy/galaxy-central/commits/fe4cfbd300a1/
Changeset: fe4cfbd300a1
Branch: release_15.03
User: dan
Date: 2015-02-27 20:50:28+00:00
Summary: Have IGV external display application load a set of links for available genomes via a tool data table that reads a URL (http://igv.broadinstitute.org/genomes/genomes.txt) The manually specified builds links should now be used to add additional builds, or for alias mapping (e.g. hg_g1k_v37-->b37).
Affected #: 4 files
diff -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 -r fe4cfbd300a11b8fc1f05fff06209035f0ef26e6 config/tool_data_table_conf.xml.sample
--- a/config/tool_data_table_conf.xml.sample
+++ b/config/tool_data_table_conf.xml.sample
@@ -65,4 +65,9 @@
<columns>value, path</columns><file path="tool-data/twobit.loc" /></table>
+ <!-- Available IGV builds, loaded from URL -->
+ <table name="igv_broad_genomes" comment_char="#">
+ <columns>name, url, value</columns>
+ <file url="http://igv.broadinstitute.org/genomes/genomes.txt" />
+ </table></tables>
diff -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 -r fe4cfbd300a11b8fc1f05fff06209035f0ef26e6 display_applications/igv/bam.xml
--- a/display_applications/igv/bam.xml
+++ b/display_applications/igv/bam.xml
@@ -93,7 +93,20 @@
#end if
</param></dynamic_links>
-
+
+
+ <dynamic_links from_data_table="igv_broad_genomes" skip_startswith="#" id="value" name="name">
+
+ <!-- Our input data table is one line per dbkey -->
+ <filter>${ $dataset.dbkey == $value }</filter>
+
+ <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+ <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bam… $bam_file.name )}</url>
+
+ <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
+ <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" />
+
+ </dynamic_links></display><!-- Dan Blankenberg -->
diff -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 -r fe4cfbd300a11b8fc1f05fff06209035f0ef26e6 display_applications/igv/vcf.xml
--- a/display_applications/igv/vcf.xml
+++ b/display_applications/igv/vcf.xml
@@ -93,7 +93,20 @@
#end if
</param></dynamic_links>
-
+
+
+ <dynamic_links from_data_table="igv_broad_genomes" skip_startswith="#" id="value" name="name">
+
+ <!-- Our input data table is one line per dbkey -->
+ <filter>${ $dataset.dbkey == $value }</filter>
+
+ <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+ <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bgz… $bgzip_file.name )}</url>
+
+ <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
+ <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
+
+ </dynamic_links></display><!-- Dan Blankenberg -->
diff -r be0aa5c296c72e85dfea2effe7d228953ffcb8a1 -r fe4cfbd300a11b8fc1f05fff06209035f0ef26e6 tool-data/shared/igv/igv_build_sites.txt.sample
--- a/tool-data/shared/igv/igv_build_sites.txt.sample
+++ b/tool-data/shared/igv/igv_build_sites.txt.sample
@@ -1,4 +1,4 @@
#site_id site_name site_url dbkey ivg_build_name
-web_link_main web current http://www.broadinstitute.org/igv/projects/current/igv.php hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
+web_link_main web current http://www.broadinstitute.org/igv/projects/current/igv.php hg_g1k_v37 b37
#web_jnlp_1.5 web 1.5 http://www.broadinstitute.org/igvdata/jws/prod hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
-#local_default local http://localhost:60151/load hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
\ No newline at end of file
+#local_default local http://localhost:60151/load hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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12 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a3be81bd096a/
Changeset: a3be81bd096a
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: Reduce use of bare excepts in install_manager.py.
Affected #: 1 file
diff -r 179c7c3fbb0db10765a97eb632bfc34c570ef0ff -r a3be81bd096a90d8a2528921d84e66d0c97479fb lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -710,19 +710,19 @@
installed_tool_shed_repositories = []
try:
has_repository_dependencies = repository_revision_dict[ 'has_repository_dependencies' ]
- except:
+ except KeyError:
raise exceptions.InternalServerError( "Tool shed response missing required parameter 'has_repository_dependencies'." )
try:
includes_tools = repository_revision_dict[ 'includes_tools' ]
- except:
+ except KeyError:
raise exceptions.InternalServerError( "Tool shed response missing required parameter 'includes_tools'." )
try:
includes_tool_dependencies = repository_revision_dict[ 'includes_tool_dependencies' ]
- except:
+ except KeyError:
raise exceptions.InternalServerError( "Tool shed response missing required parameter 'includes_tool_dependencies'." )
try:
includes_tools_for_display_in_tool_panel = repository_revision_dict[ 'includes_tools_for_display_in_tool_panel' ]
- except:
+ except KeyError:
raise exceptions.InternalServerError( "Tool shed response missing required parameter 'includes_tools_for_display_in_tool_panel'." )
# Get the information about the Galaxy components (e.g., tool pane section, tool config file, etc) that will contain the repository information.
install_repository_dependencies = install_options.get( 'install_repository_dependencies', False )
https://bitbucket.org/galaxy/galaxy-central/commits/f1ea6093d943/
Changeset: f1ea6093d943
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: Eliminate unused using_api parameter in install_manager.
Affected #: 2 files
diff -r a3be81bd096a90d8a2528921d84e66d0c97479fb -r f1ea6093d9435b2c6015c50f8a1defecbc26f8ef lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1092,7 +1092,7 @@
tool_path=tool_path,
tool_shed_url=tool_shed_url )
created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
- install_repository_manager.handle_tool_shed_repositories( installation_dict, using_api=False )
+ install_repository_manager.handle_tool_shed_repositories( installation_dict )
if created_or_updated_tool_shed_repositories:
installation_dict = dict( created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories,
filtered_repo_info_dicts=filtered_repo_info_dicts,
diff -r a3be81bd096a90d8a2528921d84e66d0c97479fb -r f1ea6093d9435b2c6015c50f8a1defecbc26f8ef lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -623,7 +623,7 @@
# Load proprietary datatype display applications
self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
- def handle_tool_shed_repositories( self, installation_dict, using_api=False ):
+ def handle_tool_shed_repositories( self, installation_dict ):
# The following installation_dict entries are all required.
install_repository_dependencies = installation_dict[ 'install_repository_dependencies' ]
new_tool_panel_section_label = installation_dict[ 'new_tool_panel_section_label' ]
@@ -759,7 +759,7 @@
tool_shed_url=tool_shed_url )
# Create the tool_shed_repository database records and gather additional information for repository installation.
created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \
- self.handle_tool_shed_repositories( installation_dict, using_api=True )
+ self.handle_tool_shed_repositories( installation_dict )
if created_or_updated_tool_shed_repositories:
# Build the dictionary of information necessary for installing the repositories.
installation_dict = dict( created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories,
https://bitbucket.org/galaxy/galaxy-central/commits/f95ba7774644/
Changeset: f95ba7774644
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: Small refactoring of install_manager.py.
Break tool dependency dir checking out into its own function to reduce complexity of __install_repositories.
Affected #: 1 file
diff -r f1ea6093d9435b2c6015c50f8a1defecbc26f8ef -r f95ba77746449eeff2593a06a457b57ebe803eca lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -728,11 +728,7 @@
install_repository_dependencies = install_options.get( 'install_repository_dependencies', False )
install_tool_dependencies = install_options.get( 'install_tool_dependencies', False )
if install_tool_dependencies:
- if self.app.config.tool_dependency_dir is None:
- no_tool_dependency_dir_message = "Tool dependencies can be automatically installed only if you set "
- no_tool_dependency_dir_message += "the value of your 'tool_dependency_dir' setting in your Galaxy "
- no_tool_dependency_dir_message += "configuration file (galaxy.ini) and restart your Galaxy server. "
- raise exceptions.ConfigDoesNotAllowException( no_tool_dependency_dir_message )
+ self.__assert_can_install_dependencies()
new_tool_panel_section_label = install_options.get( 'new_tool_panel_section_label', '' )
shed_tool_conf = install_options.get( 'shed_tool_conf', None )
if shed_tool_conf:
@@ -957,6 +953,13 @@
self.install_model.context.add( tool_shed_repository )
self.install_model.context.flush()
+ def __assert_can_install_dependencies(self):
+ if self.app.config.tool_dependency_dir is None:
+ no_tool_dependency_dir_message = "Tool dependencies can be automatically installed only if you set "
+ no_tool_dependency_dir_message += "the value of your 'tool_dependency_dir' setting in your Galaxy "
+ no_tool_dependency_dir_message += "configuration file (galaxy.ini) and restart your Galaxy server. "
+ raise exceptions.ConfigDoesNotAllowException( no_tool_dependency_dir_message )
+
def fetch_tool_versions( app, tool_shed_repository ):
""" Fetch a data structure describing tool shed versions from the tool shed
https://bitbucket.org/galaxy/galaxy-central/commits/0688265255e4/
Changeset: 0688265255e4
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: Make more clear function in admin_toolshed is not entry point.
Affected #: 1 file
diff -r f95ba77746449eeff2593a06a457b57ebe803eca -r 0688265255e47eea3e90ce0947cadc520ab1145f lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -639,32 +639,6 @@
@web.expose
@web.require_admin
- def install_tool_shed_repositories( self, trans, tool_shed_repositories, reinstalling=False, **kwd ):
- """Install specified tool shed repositories."""
- shed_tool_conf = kwd.get( 'shed_tool_conf', '' )
- tool_path = kwd[ 'tool_path' ]
- install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
- # There must be a one-to-one mapping between items in the 3 lists: tool_shed_repositories, tool_panel_section_keys, repo_info_dicts.
- tool_panel_section_keys = util.listify( kwd[ 'tool_panel_section_keys' ] )
- repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] )
- irm = install_manager.InstallRepositoryManager( trans.app )
- for index, tool_shed_repository in enumerate( tool_shed_repositories ):
- repo_info_dict = repo_info_dicts[ index ]
- tool_panel_section_key = tool_panel_section_keys[ index ]
- irm.install_tool_shed_repository( tool_shed_repository,
- repo_info_dict,
- tool_panel_section_key,
- shed_tool_conf,
- tool_path,
- install_tool_dependencies,
- reinstalling=reinstalling )
- tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ]
- return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
- action='monitor_repository_installation',
- tool_shed_repository_ids=tsr_ids_for_monitoring ) )
-
- @web.expose
- @web.require_admin
def manage_repositories( self, trans, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
@@ -733,10 +707,10 @@
if repositories_for_installation:
decoded_kwd[ 'repo_info_dicts' ] = filtered_repo_info_dicts
decoded_kwd[ 'tool_panel_section_keys' ] = filtered_tool_panel_section_keys
- self.install_tool_shed_repositories( trans,
- repositories_for_installation,
- reinstalling=reinstalling,
- **decoded_kwd )
+ self.__install_tool_shed_repositories( trans,
+ repositories_for_installation,
+ reinstalling=reinstalling,
+ **decoded_kwd )
else:
kwd[ 'message' ] = 'All selected tool shed repositories are already installed.'
kwd[ 'status' ] = 'error'
@@ -2162,3 +2136,27 @@
metadata=metadata,
message=message,
status=status )
+
+ def __install_tool_shed_repositories( self, trans, tool_shed_repositories, reinstalling=False, **kwd ):
+ """Install specified tool shed repositories."""
+ shed_tool_conf = kwd.get( 'shed_tool_conf', '' )
+ tool_path = kwd[ 'tool_path' ]
+ install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
+ # There must be a one-to-one mapping between items in the 3 lists: tool_shed_repositories, tool_panel_section_keys, repo_info_dicts.
+ tool_panel_section_keys = util.listify( kwd[ 'tool_panel_section_keys' ] )
+ repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] )
+ irm = install_manager.InstallRepositoryManager( trans.app )
+ for index, tool_shed_repository in enumerate( tool_shed_repositories ):
+ repo_info_dict = repo_info_dicts[ index ]
+ tool_panel_section_key = tool_panel_section_keys[ index ]
+ irm.install_tool_shed_repository( tool_shed_repository,
+ repo_info_dict,
+ tool_panel_section_key,
+ shed_tool_conf,
+ tool_path,
+ install_tool_dependencies,
+ reinstalling=reinstalling )
+ tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ]
+ return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+ action='monitor_repository_installation',
+ tool_shed_repository_ids=tsr_ids_for_monitoring ) )
https://bitbucket.org/galaxy/galaxy-central/commits/2998ac978d89/
Changeset: 2998ac978d89
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: Extract an exception out in install_manager.py.
Will make it easier to catch this specific problem in admin_toolshed in subsequent refactoring.
Affected #: 1 file
diff -r 0688265255e47eea3e90ce0947cadc520ab1145f -r 2998ac978d8935c7d9ba655ada297e2f2d205ebd lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -804,7 +804,7 @@
installed_tool_shed_repositories.append( tool_shed_repository )
else:
# We're attempting to install more than 1 repository, and all of them have already been installed.
- raise exceptions.RequestParameterInvalidException( 'All repositories that you are attempting to install have been previously installed.' )
+ raise RepositoriesInstalledException()
return installed_tool_shed_repositories
def install_tool_shed_repository( self, tool_shed_repository, repo_info_dict, tool_panel_section_key, shed_tool_conf, tool_path,
@@ -961,6 +961,12 @@
raise exceptions.ConfigDoesNotAllowException( no_tool_dependency_dir_message )
+class RepositoriesInstalledException(exceptions.RequestParameterInvalidException):
+
+ def __init__(self):
+ super(RepositoriesInstalledException, self).__init__('All repositories that you are attempting to install have been previously installed.')
+
+
def fetch_tool_versions( app, tool_shed_repository ):
""" Fetch a data structure describing tool shed versions from the tool shed
corresponding to a tool_shed_repository object.
https://bitbucket.org/galaxy/galaxy-central/commits/d7849c8a5de0/
Changeset: d7849c8a5de0
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: Refactor a bunch of repository installation out of controller...
... and into install_manager.py. There is a bunch of duplication between this and the code already in install manager - which is a good indication this is where it belongs - hopefully we can de-duplicate it with subsequent changes. This will also allow more of install_manager's methods to be marked as internal.
Affected #: 2 files
diff -r 2998ac978d8935c7d9ba655ada297e2f2d205ebd -r d7849c8a5de0878a9da97ce4ab52a0272a904a13 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -678,41 +678,20 @@
reinstalling = util.string_as_bool( kwd.get( 'reinstalling', False ) )
encoded_kwd = kwd[ 'encoded_kwd' ]
decoded_kwd = encoding_util.tool_shed_decode( encoded_kwd )
- tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ]
- tool_panel_section_keys = decoded_kwd[ 'tool_panel_section_keys' ]
- repo_info_dicts = decoded_kwd[ 'repo_info_dicts' ]
- filtered_repo_info_dicts = []
- filtered_tool_panel_section_keys = []
- repositories_for_installation = []
- # Some repositories may have repository dependencies that are required to be installed before the
- # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in the
- # required order.
- ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \
- irm.order_components_for_installation( tsr_ids,
- repo_info_dicts,
- tool_panel_section_keys=tool_panel_section_keys )
- for tsr_id in ordered_tsr_ids:
- repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \
- .get( trans.security.decode_id( tsr_id ) )
- if repository.status in [ trans.install_model.ToolShedRepository.installation_status.NEW,
- trans.install_model.ToolShedRepository.installation_status.UNINSTALLED ]:
- repositories_for_installation.append( repository )
- repo_info_dict, tool_panel_section_key = \
- irm.get_repository_components_for_installation( tsr_id,
- ordered_tsr_ids,
- ordered_repo_info_dicts,
- ordered_tool_panel_section_keys )
- filtered_repo_info_dicts.append( repo_info_dict )
- filtered_tool_panel_section_keys.append( tool_panel_section_key )
- if repositories_for_installation:
- decoded_kwd[ 'repo_info_dicts' ] = filtered_repo_info_dicts
- decoded_kwd[ 'tool_panel_section_keys' ] = filtered_tool_panel_section_keys
- self.__install_tool_shed_repositories( trans,
- repositories_for_installation,
- reinstalling=reinstalling,
- **decoded_kwd )
- else:
- kwd[ 'message' ] = 'All selected tool shed repositories are already installed.'
+ install_tool_dependencies = CheckboxField.is_checked( decoded_kwd.get( 'install_tool_dependencies', '' ) )
+ decoded_kwd['install_tool_dependencies'] = install_tool_dependencies
+ try:
+ tool_shed_repositories = irm.install_web(
+ trans=trans,
+ decoded_kwd=decoded_kwd,
+ reinstalling=reinstalling,
+ )
+ tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ]
+ trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+ action='monitor_repository_installation',
+ tool_shed_repository_ids=tsr_ids_for_monitoring ) )
+ except install_manager.RepositoriesInstalledException as e:
+ kwd[ 'message' ] = e.message
kwd[ 'status' ] = 'error'
return self.repository_installation_grid( trans, **kwd )
@@ -2136,27 +2115,3 @@
metadata=metadata,
message=message,
status=status )
-
- def __install_tool_shed_repositories( self, trans, tool_shed_repositories, reinstalling=False, **kwd ):
- """Install specified tool shed repositories."""
- shed_tool_conf = kwd.get( 'shed_tool_conf', '' )
- tool_path = kwd[ 'tool_path' ]
- install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
- # There must be a one-to-one mapping between items in the 3 lists: tool_shed_repositories, tool_panel_section_keys, repo_info_dicts.
- tool_panel_section_keys = util.listify( kwd[ 'tool_panel_section_keys' ] )
- repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] )
- irm = install_manager.InstallRepositoryManager( trans.app )
- for index, tool_shed_repository in enumerate( tool_shed_repositories ):
- repo_info_dict = repo_info_dicts[ index ]
- tool_panel_section_key = tool_panel_section_keys[ index ]
- irm.install_tool_shed_repository( tool_shed_repository,
- repo_info_dict,
- tool_panel_section_key,
- shed_tool_conf,
- tool_path,
- install_tool_dependencies,
- reinstalling=reinstalling )
- tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ]
- return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
- action='monitor_repository_installation',
- tool_shed_repository_ids=tsr_ids_for_monitoring ) )
diff -r 2998ac978d8935c7d9ba655ada297e2f2d205ebd -r d7849c8a5de0878a9da97ce4ab52a0272a904a13 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -7,6 +7,7 @@
from galaxy import exceptions
from galaxy import eggs
+from galaxy import util
eggs.require( 'paramiko' )
eggs.require( 'ssh' )
@@ -807,6 +808,54 @@
raise RepositoriesInstalledException()
return installed_tool_shed_repositories
+ def install_web( self, trans, decoded_kwd, reinstalling ):
+ shed_tool_conf = decoded_kwd.get( 'shed_tool_conf', '' )
+ tool_path = decoded_kwd[ 'tool_path' ]
+ tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ]
+ tool_panel_section_keys = util.listify( decoded_kwd[ 'tool_panel_section_keys' ] )
+ repo_info_dicts = util.listify( decoded_kwd[ 'repo_info_dicts' ] )
+ install_tool_dependencies = decoded_kwd['install_tool_dependencies']
+ filtered_repo_info_dicts = []
+ filtered_tool_panel_section_keys = []
+ repositories_for_installation = []
+ # Some repositories may have repository dependencies that are required to be installed before the
+ # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in the
+ # required order.
+ ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \
+ self.order_components_for_installation( tsr_ids,
+ repo_info_dicts,
+ tool_panel_section_keys=tool_panel_section_keys )
+ for tsr_id in ordered_tsr_ids:
+ repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \
+ .get( trans.security.decode_id( tsr_id ) )
+ if repository.status in [ trans.install_model.ToolShedRepository.installation_status.NEW,
+ trans.install_model.ToolShedRepository.installation_status.UNINSTALLED ]:
+ repositories_for_installation.append( repository )
+ repo_info_dict, tool_panel_section_key = \
+ self.get_repository_components_for_installation( tsr_id,
+ ordered_tsr_ids,
+ ordered_repo_info_dicts,
+ ordered_tool_panel_section_keys )
+ filtered_repo_info_dicts.append( repo_info_dict )
+ filtered_tool_panel_section_keys.append( tool_panel_section_key )
+
+ installed_tool_shed_repositories = []
+ if repositories_for_installation:
+ for index, tool_shed_repository in enumerate( repositories_for_installation ):
+ repo_info_dict = filtered_repo_info_dicts[ index ]
+ tool_panel_section_key = filtered_tool_panel_section_keys[ index ]
+ self.install_tool_shed_repository( tool_shed_repository,
+ repo_info_dict=repo_info_dict,
+ tool_panel_section_key=tool_panel_section_key,
+ shed_tool_conf=shed_tool_conf,
+ tool_path=tool_path,
+ install_tool_dependencies=install_tool_dependencies,
+ reinstalling=reinstalling )
+ installed_tool_shed_repositories.append( tool_shed_repository )
+ else:
+ raise RepositoriesInstalledException()
+ return installed_tool_shed_repositories
+
def install_tool_shed_repository( self, tool_shed_repository, repo_info_dict, tool_panel_section_key, shed_tool_conf, tool_path,
install_tool_dependencies, reinstalling=False ):
if tool_panel_section_key:
https://bitbucket.org/galaxy/galaxy-central/commits/4a04ee11725e/
Changeset: 4a04ee11725e
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: PEP-8 comments in install_manager.py.
Affected #: 1 file
diff -r d7849c8a5de0878a9da97ce4ab52a0272a904a13 -r 4a04ee11725e11127848775ae46e68818843e768 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -455,10 +455,12 @@
def get_repository_components_for_installation( self, encoded_tsr_id, encoded_tsr_ids, repo_info_dicts,
tool_panel_section_keys ):
"""
- The received encoded_tsr_ids, repo_info_dicts, and tool_panel_section_keys are 3 lists that
- contain associated elements at each location in the list. This method will return the elements
- from repo_info_dicts and tool_panel_section_keys associated with the received encoded_tsr_id
- by determining its location in the received encoded_tsr_ids list.
+ The received encoded_tsr_ids, repo_info_dicts, and
+ tool_panel_section_keys are 3 lists that contain associated elements
+ at each location in the list. This method will return the elements
+ from repo_info_dicts and tool_panel_section_keys associated with the
+ received encoded_tsr_id by determining its location in the received
+ encoded_tsr_ids list.
"""
for index, tsr_id in enumerate( encoded_tsr_ids ):
if tsr_id == encoded_tsr_id:
@@ -775,15 +777,18 @@
tool_panel_section_keys=tool_panel_section_keys,
tool_path=tool_path,
tool_shed_url=tool_shed_url )
- # Prepare the repositories for installation. Even though this method receives a single combination
- # of tool_shed_url, name, owner and changeset_revision, there may be multiple repositories for installation
- # at this point because repository dependencies may have added additional repositories for installation
- # along with the single specified repository.
+ # Prepare the repositories for installation. Even though this
+ # method receives a single combination of tool_shed_url, name,
+ # owner and changeset_revision, there may be multiple repositories
+ # for installation at this point because repository dependencies
+ # may have added additional repositories for installation along
+ # with the single specified repository.
encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \
self.initiate_repository_installation( installation_dict )
- # Some repositories may have repository dependencies that are required to be installed before the
- # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in
- # the required order.
+ # Some repositories may have repository dependencies that are
+ # required to be installed before the dependent repository, so
+ # we'll order the list of tsr_ids to ensure all repositories
+ # install in the required order.
tsr_ids = [ self.app.security.encode_id( tool_shed_repository.id ) for tool_shed_repository in tool_shed_repositories ]
ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \
self.order_components_for_installation( tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys )
https://bitbucket.org/galaxy/galaxy-central/commits/77c9941c3d8b/
Changeset: 77c9941c3d8b
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: Refactor __install_repositories so it looks more like newer install_web.
Affected #: 1 file
diff -r 4a04ee11725e11127848775ae46e68818843e768 -r 77c9941c3d8befb3d2678862633f05216cca1c18 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -709,8 +709,6 @@
return installed_tool_shed_repositories
def __install_repositories( self, tool_shed_url, repository_revision_dict, repo_info_dicts, install_options ):
- # Keep track of all repositories that are installed - there may be more than one if repository dependencies are installed.
- installed_tool_shed_repositories = []
try:
has_repository_dependencies = repository_revision_dict[ 'has_repository_dependencies' ]
except KeyError:
@@ -790,6 +788,10 @@
# we'll order the list of tsr_ids to ensure all repositories
# install in the required order.
tsr_ids = [ self.app.security.encode_id( tool_shed_repository.id ) for tool_shed_repository in tool_shed_repositories ]
+
+ # Keep track of all repositories that are installed - there may be more than one if repository dependencies are installed.
+ installed_tool_shed_repositories = []
+
ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \
self.order_components_for_installation( tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys )
# Install the repositories, keeping track of each one for later display.
@@ -808,10 +810,10 @@
install_tool_dependencies,
reinstalling=False )
installed_tool_shed_repositories.append( tool_shed_repository )
+ return installed_tool_shed_repositories
else:
# We're attempting to install more than 1 repository, and all of them have already been installed.
raise RepositoriesInstalledException()
- return installed_tool_shed_repositories
def install_web( self, trans, decoded_kwd, reinstalling ):
shed_tool_conf = decoded_kwd.get( 'shed_tool_conf', '' )
https://bitbucket.org/galaxy/galaxy-central/commits/1b96a2122ea6/
Changeset: 1b96a2122ea6
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: Eliminate duplication between ts installing from API and web controller.
Favoring the web controller variant slightly - it is known to work better and has test coverage.
Affected #: 2 files
diff -r 77c9941c3d8befb3d2678862633f05216cca1c18 -r 1b96a2122ea6607e84e3fb89e5e9209fbd119fd4 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -679,10 +679,11 @@
encoded_kwd = kwd[ 'encoded_kwd' ]
decoded_kwd = encoding_util.tool_shed_decode( encoded_kwd )
install_tool_dependencies = CheckboxField.is_checked( decoded_kwd.get( 'install_tool_dependencies', '' ) )
+ tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ]
decoded_kwd['install_tool_dependencies'] = install_tool_dependencies
try:
- tool_shed_repositories = irm.install_web(
- trans=trans,
+ tool_shed_repositories = irm.install_repositories(
+ tsr_ids=tsr_ids,
decoded_kwd=decoded_kwd,
reinstalling=reinstalling,
)
diff -r 77c9941c3d8befb3d2678862633f05216cca1c18 -r 1b96a2122ea6607e84e3fb89e5e9209fbd119fd4 lib/tool_shed/galaxy_install/install_manager.py
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -702,13 +702,15 @@
name,
owner,
changeset_revision )
- installed_tool_shed_repositories = self.__install_repositories( tool_shed_url,
- repository_revision_dict,
- repo_info_dicts,
- install_options )
+ installed_tool_shed_repositories = self.__initiate_and_install_repositories(
+ tool_shed_url,
+ repository_revision_dict,
+ repo_info_dicts,
+ install_options
+ )
return installed_tool_shed_repositories
- def __install_repositories( self, tool_shed_url, repository_revision_dict, repo_info_dicts, install_options ):
+ def __initiate_and_install_repositories( self, tool_shed_url, repository_revision_dict, repo_info_dicts, install_options ):
try:
has_repository_dependencies = repository_revision_dict[ 'has_repository_dependencies' ]
except KeyError:
@@ -789,36 +791,18 @@
# install in the required order.
tsr_ids = [ self.app.security.encode_id( tool_shed_repository.id ) for tool_shed_repository in tool_shed_repositories ]
- # Keep track of all repositories that are installed - there may be more than one if repository dependencies are installed.
- installed_tool_shed_repositories = []
+ decoded_kwd = dict(
+ shed_tool_conf=shed_tool_conf,
+ tool_path=tool_path,
+ tool_panel_section_keys=tool_panel_section_keys,
+ repo_info_dicts=repo_info_dicts,
+ install_tool_dependencies=install_tool_dependencies,
+ )
+ return self.install_repositories(tsr_ids, decoded_kwd, reinstalling=False)
- ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \
- self.order_components_for_installation( tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys )
- # Install the repositories, keeping track of each one for later display.
- for index, tsr_id in enumerate( ordered_tsr_ids ):
- tool_shed_repository = self.install_model.context.query( self.install_model.ToolShedRepository ) \
- .get( self.app.security.decode_id( tsr_id ) )
- if tool_shed_repository.status in [ self.install_model.ToolShedRepository.installation_status.NEW,
- self.install_model.ToolShedRepository.installation_status.UNINSTALLED ]:
- repo_info_dict = ordered_repo_info_dicts[ index ]
- tool_panel_section_key = ordered_tool_panel_section_keys[ index ]
- self.install_tool_shed_repository( tool_shed_repository,
- repo_info_dict,
- tool_panel_section_key,
- shed_tool_conf,
- tool_path,
- install_tool_dependencies,
- reinstalling=False )
- installed_tool_shed_repositories.append( tool_shed_repository )
- return installed_tool_shed_repositories
- else:
- # We're attempting to install more than 1 repository, and all of them have already been installed.
- raise RepositoriesInstalledException()
-
- def install_web( self, trans, decoded_kwd, reinstalling ):
+ def install_repositories( self, tsr_ids, decoded_kwd, reinstalling ):
shed_tool_conf = decoded_kwd.get( 'shed_tool_conf', '' )
tool_path = decoded_kwd[ 'tool_path' ]
- tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ]
tool_panel_section_keys = util.listify( decoded_kwd[ 'tool_panel_section_keys' ] )
repo_info_dicts = util.listify( decoded_kwd[ 'repo_info_dicts' ] )
install_tool_dependencies = decoded_kwd['install_tool_dependencies']
@@ -833,10 +817,10 @@
repo_info_dicts,
tool_panel_section_keys=tool_panel_section_keys )
for tsr_id in ordered_tsr_ids:
- repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \
- .get( trans.security.decode_id( tsr_id ) )
- if repository.status in [ trans.install_model.ToolShedRepository.installation_status.NEW,
- trans.install_model.ToolShedRepository.installation_status.UNINSTALLED ]:
+ repository = self.install_model.context.query( self.install_model.ToolShedRepository ) \
+ .get( self.app.security.decode_id( tsr_id ) )
+ if repository.status in [ self.install_model.ToolShedRepository.installation_status.NEW,
+ self.install_model.ToolShedRepository.installation_status.UNINSTALLED ]:
repositories_for_installation.append( repository )
repo_info_dict, tool_panel_section_key = \
self.get_repository_components_for_installation( tsr_id,
https://bitbucket.org/galaxy/galaxy-central/commits/ebe2008f5e49/
Changeset: ebe2008f5e49
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: Use append_section abstraction.
Affected #: 1 file
diff -r 1b96a2122ea6607e84e3fb89e5e9209fbd119fd4 -r ebe2008f5e49998cc74264ee085e7e7a4fab57bc lib/galaxy/tools/toolbox/base.py
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -237,7 +237,7 @@
'version': '',
}
tool_section = ToolSection( section_dict )
- self._tool_panel[ tool_panel_section_key ] = tool_section
+ self._tool_panel.append_section( tool_panel_section_key, tool_section )
log.debug( "Loading new tool panel section: %s" % str( tool_section.name ) )
else:
tool_section = None
https://bitbucket.org/galaxy/galaxy-central/commits/4f0678e797a1/
Changeset: 4f0678e797a1
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: PEP-8 in toolbox/base.py.
Affected #: 1 file
diff -r ebe2008f5e49998cc74264ee085e7e7a4fab57bc -r 4f0678e797a1247103459fba186c4dc8765b8aa2 lib/galaxy/tools/toolbox/base.py
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -457,9 +457,9 @@
if tool_id in self._tools_by_id and not get_all_versions:
if tool_version and tool_version in self._tool_versions_by_id[ tool_id ]:
return self._tool_versions_by_id[ tool_id ][ tool_version ]
- #tool_id exactly matches an available tool by id (which is 'old' tool_id or guid)
+ # tool_id exactly matches an available tool by id (which is 'old' tool_id or guid)
return self._tools_by_id[ tool_id ]
- #exact tool id match not found, or all versions requested, search for other options, e.g. migrated tools or different versions
+ # exact tool id match not found, or all versions requested, search for other options, e.g. migrated tools or different versions
rval = []
tool_lineage = self._lineage_map.get( tool_id )
if tool_lineage:
@@ -469,7 +469,7 @@
if lineage_tool:
rval.append( lineage_tool )
if not rval:
- #still no tool, do a deeper search and try to match by old ids
+ # still no tool, do a deeper search and try to match by old ids
for tool in self._tools_by_id.itervalues():
if tool.old_id == tool_id:
rval.append( tool )
@@ -478,14 +478,14 @@
return rval
else:
if tool_version:
- #return first tool with matching version
+ # return first tool with matching version
for tool in rval:
if tool.version == tool_version:
return tool
- #No tool matches by version, simply return the first available tool found
+ # No tool matches by version, simply return the first available tool found
return rval[0]
- #We now likely have a Toolshed guid passed in, but no supporting database entries
- #If the tool exists by exact id and is loaded then provide exact match within a list
+ # We now likely have a Toolshed guid passed in, but no supporting database entries
+ # If the tool exists by exact id and is loaded then provide exact match within a list
if tool_id in self._tools_by_id:
return[ self._tools_by_id[ tool_id ] ]
return None
@@ -1012,7 +1012,7 @@
break
if tool_id in self.data_manager_tools:
del self.data_manager_tools[ tool_id ]
- #TODO: do we need to manually remove from the integrated panel here?
+ # TODO: do we need to manually remove from the integrated panel here?
message = "Removed the tool:<br/>"
message += "<b>name:</b> %s<br/>" % tool.name
message += "<b>id:</b> %s<br/>" % tool.id
https://bitbucket.org/galaxy/galaxy-central/commits/0468d285f89c/
Changeset: 0468d285f89c
User: jmchilton
Date: 2015-02-27 20:58:02+00:00
Summary: Move integrated tool panel logic into its own module/mixin.
Affected #: 2 files
diff -r 4f0678e797a1247103459fba186c4dc8765b8aa2 -r 0468d285f89c799559926c94f300c42d05e8c47a lib/galaxy/tools/toolbox/base.py
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -1,6 +1,5 @@
import os
import re
-import shutil
import string
import tarfile
import tempfile
@@ -23,6 +22,7 @@
from .panel import ToolSectionLabel
from .panel import ToolSection
from .panel import panel_item_types
+from .integrated_panel import ManagesIntegratedToolPanelMixin
from .lineages import LineageMap
from .tags import tool_tag_manager
@@ -37,22 +37,7 @@
log = logging.getLogger( __name__ )
-INTEGRATED_TOOL_PANEL_DESCRIPTION = """
-This is Galaxy's integrated tool panel and should be modified directly only for
-reordering tools inside a section. Each time Galaxy starts up, this file is
-synchronized with the various tool config files: tools, sections and labels
-added to one of these files, will be added also here in the appropriate place,
-while elements removed from the tool config files will be correspondingly
-deleted from this file.
-To modify locally managed tools (e.g. from tool_conf.xml) modify that file
-directly and restart Galaxy. Whenever possible Tool Shed managed tools (e.g.
-from shed_tool_conf.xml) should be managed from within the Galaxy interface or
-via its API - but if changes are necessary (such as to hide a tool or re-assign
-its section) modify that file and restart Galaxy.
-"""
-
-
-class AbstractToolBox( object, Dictifiable ):
+class AbstractToolBox( object, Dictifiable, ManagesIntegratedToolPanelMixin ):
"""
Abstract container for managing a ToolPanel - containing tools and
workflows optionally in labelled sections.
@@ -78,15 +63,8 @@
self._index = 0
self.data_manager_tools = odict()
self._lineage_map = LineageMap( app )
- # File that contains the XML section and tool tags from all tool panel config files integrated into a
- # single file that defines the tool panel layout. This file can be changed by the Galaxy administrator
- # (in a way similar to the single tool_conf.xml file in the past) to alter the layout of the tool panel.
- self._integrated_tool_panel_config = app.config.integrated_tool_panel_config
- # In-memory dictionary that defines the layout of the tool_panel.xml file on disk.
- self._integrated_tool_panel = ToolPanelElements()
- self._integrated_tool_panel_config_has_contents = os.path.exists( self._integrated_tool_panel_config ) and os.stat( self._integrated_tool_panel_config ).st_size > 0
- if self._integrated_tool_panel_config_has_contents:
- self._load_integrated_tool_panel_keys()
+ # Sets self._integrated_tool_panel and self._integrated_tool_panel_config_has_contents
+ self._init_integrated_tool_panel( app.config )
# The following refers to the tool_path config setting for backward compatibility. The shed-related
# (e.g., shed_tool_conf.xml) files include the tool_path attribute within the <toolbox> tag.
self._tool_root_dir = tool_root_dir
@@ -98,12 +76,7 @@
if self.app.name == 'galaxy' and self._integrated_tool_panel_config_has_contents:
# Load self._tool_panel based on the order in self._integrated_tool_panel.
self._load_tool_panel()
- if app.config.update_integrated_tool_panel:
- # Write the current in-memory integrated_tool_panel to the integrated_tool_panel.xml file.
- # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel
- # config files, adding or removing locally developed tools or workflows. The value of integrated_tool_panel
- # will be False when things like functional tests are the caller.
- self._write_integrated_tool_panel_config_file()
+ self._save_integrated_tool_panel()
def create_tool( self, config_file, repository_id=None, guid=None, **kwds ):
raise NotImplementedError()
@@ -215,9 +188,8 @@
for index, my_shed_tool_conf in enumerate( self._dynamic_tool_confs ):
if shed_conf['config_filename'] == my_shed_tool_conf['config_filename']:
self._dynamic_tool_confs[ index ] = shed_conf
- if integrated_panel_changes and app.config.update_integrated_tool_panel:
- # Write the current in-memory version of the integrated_tool_panel.xml file to disk.
- self._write_integrated_tool_panel_config_file()
+ if integrated_panel_changes:
+ self._save_integrated_tool_panel()
app.reindex_tool_search()
def get_section( self, section_id, new_label=None, create_if_needed=False ):
@@ -400,52 +372,6 @@
elif elem.tag == 'label':
self._integrated_tool_panel.stub_label( key )
- def _write_integrated_tool_panel_config_file( self ):
- """
- Write the current in-memory version of the integrated_tool_panel.xml file to disk. Since Galaxy administrators
- use this file to manage the tool panel, we'll not use xml_to_string() since it doesn't write XML quite right.
- """
- fd, filename = tempfile.mkstemp()
- os.write( fd, '<?xml version="1.0"?>\n' )
- os.write( fd, '<toolbox>\n' )
- os.write( fd, ' <!--\n ')
- os.write( fd, '\n '.join( [ l for l in INTEGRATED_TOOL_PANEL_DESCRIPTION.split("\n") if l ] ) )
- os.write( fd, '\n -->\n')
- for key, item_type, item in self._integrated_tool_panel.panel_items_iter():
- if item:
- if item_type == panel_item_types.TOOL:
- os.write( fd, ' <tool id="%s" />\n' % item.id )
- elif item_type == panel_item_types.WORKFLOW:
- os.write( fd, ' <workflow id="%s" />\n' % item.id )
- elif item_type == panel_item_types.LABEL:
- label_id = item.id or ''
- label_text = item.text or ''
- label_version = item.version or ''
- os.write( fd, ' <label id="%s" text="%s" version="%s" />\n' % ( label_id, label_text, label_version ) )
- elif item_type == panel_item_types.SECTION:
- section_id = item.id or ''
- section_name = item.name or ''
- section_version = item.version or ''
- os.write( fd, ' <section id="%s" name="%s" version="%s">\n' % ( section_id, section_name, section_version ) )
- for section_key, section_item_type, section_item in item.panel_items_iter():
- if section_item_type == panel_item_types.TOOL:
- if section_item:
- os.write( fd, ' <tool id="%s" />\n' % section_item.id )
- elif section_item_type == panel_item_types.WORKFLOW:
- if section_item:
- os.write( fd, ' <workflow id="%s" />\n' % section_item.id )
- elif section_item_type == panel_item_types.LABEL:
- if section_item:
- label_id = section_item.id or ''
- label_text = section_item.text or ''
- label_version = section_item.version or ''
- os.write( fd, ' <label id="%s" text="%s" version="%s" />\n' % ( label_id, label_text, label_version ) )
- os.write( fd, ' </section>\n' )
- os.write( fd, '</toolbox>\n' )
- os.close( fd )
- shutil.move( filename, os.path.abspath( self._integrated_tool_panel_config ) )
- os.chmod( self._integrated_tool_panel_config, 0644 )
-
def get_tool( self, tool_id, tool_version=None, get_all_versions=False, exact=False ):
"""Attempt to locate a tool in the tool box."""
if tool_version:
@@ -777,13 +703,7 @@
if async:
self._load_tool_panel()
-
- if self.app.config.update_integrated_tool_panel:
- # Write the current in-memory integrated_tool_panel to the integrated_tool_panel.xml file.
- # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel
- # config files, adding or removing locally developed tools or workflows. The value of integrated_tool_panel
- # will be False when things like functional tests are the caller.
- self._write_integrated_tool_panel_config_file()
+ self._save_integrated_tool_panel()
return tool.id
except Exception:
log.exception("Failed to load potential tool %s." % tool_file)
diff -r 4f0678e797a1247103459fba186c4dc8765b8aa2 -r 0468d285f89c799559926c94f300c42d05e8c47a lib/galaxy/tools/toolbox/integrated_panel.py
--- /dev/null
+++ b/lib/galaxy/tools/toolbox/integrated_panel.py
@@ -0,0 +1,87 @@
+import os
+import shutil
+import tempfile
+
+from .panel import ToolPanelElements
+from .panel import panel_item_types
+
+
+INTEGRATED_TOOL_PANEL_DESCRIPTION = """
+This is Galaxy's integrated tool panel and should be modified directly only for
+reordering tools inside a section. Each time Galaxy starts up, this file is
+synchronized with the various tool config files: tools, sections and labels
+added to one of these files, will be added also here in the appropriate place,
+while elements removed from the tool config files will be correspondingly
+deleted from this file.
+To modify locally managed tools (e.g. from tool_conf.xml) modify that file
+directly and restart Galaxy. Whenever possible Tool Shed managed tools (e.g.
+from shed_tool_conf.xml) should be managed from within the Galaxy interface or
+via its API - but if changes are necessary (such as to hide a tool or re-assign
+its section) modify that file and restart Galaxy.
+"""
+
+
+class ManagesIntegratedToolPanelMixin:
+
+ def _init_integrated_tool_panel(self, config):
+ self.update_integrated_tool_panel = config.update_integrated_tool_panel
+ self._integrated_tool_panel_config = config.integrated_tool_panel_config
+ # In-memory dictionary that defines the layout of the tool_panel.xml file on disk.
+ self._integrated_tool_panel = ToolPanelElements()
+ self._integrated_tool_panel_config_has_contents = os.path.exists( self._integrated_tool_panel_config ) and os.stat( self._integrated_tool_panel_config ).st_size > 0
+ if self._integrated_tool_panel_config_has_contents:
+ self._load_integrated_tool_panel_keys()
+
+ def _save_integrated_tool_panel(self):
+ if self.update_integrated_tool_panel:
+ # Write the current in-memory integrated_tool_panel to the integrated_tool_panel.xml file.
+ # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel
+ # config files, adding or removing locally developed tools or workflows. The value of integrated_tool_panel
+ # will be False when things like functional tests are the caller.
+ self._write_integrated_tool_panel_config_file()
+
+ def _write_integrated_tool_panel_config_file( self ):
+ """
+ Write the current in-memory version of the integrated_tool_panel.xml file to disk. Since Galaxy administrators
+ use this file to manage the tool panel, we'll not use xml_to_string() since it doesn't write XML quite right.
+ """
+ fd, filename = tempfile.mkstemp()
+ os.write( fd, '<?xml version="1.0"?>\n' )
+ os.write( fd, '<toolbox>\n' )
+ os.write( fd, ' <!--\n ')
+ os.write( fd, '\n '.join( [ l for l in INTEGRATED_TOOL_PANEL_DESCRIPTION.split("\n") if l ] ) )
+ os.write( fd, '\n -->\n')
+ for key, item_type, item in self._integrated_tool_panel.panel_items_iter():
+ if item:
+ if item_type == panel_item_types.TOOL:
+ os.write( fd, ' <tool id="%s" />\n' % item.id )
+ elif item_type == panel_item_types.WORKFLOW:
+ os.write( fd, ' <workflow id="%s" />\n' % item.id )
+ elif item_type == panel_item_types.LABEL:
+ label_id = item.id or ''
+ label_text = item.text or ''
+ label_version = item.version or ''
+ os.write( fd, ' <label id="%s" text="%s" version="%s" />\n' % ( label_id, label_text, label_version ) )
+ elif item_type == panel_item_types.SECTION:
+ section_id = item.id or ''
+ section_name = item.name or ''
+ section_version = item.version or ''
+ os.write( fd, ' <section id="%s" name="%s" version="%s">\n' % ( section_id, section_name, section_version ) )
+ for section_key, section_item_type, section_item in item.panel_items_iter():
+ if section_item_type == panel_item_types.TOOL:
+ if section_item:
+ os.write( fd, ' <tool id="%s" />\n' % section_item.id )
+ elif section_item_type == panel_item_types.WORKFLOW:
+ if section_item:
+ os.write( fd, ' <workflow id="%s" />\n' % section_item.id )
+ elif section_item_type == panel_item_types.LABEL:
+ if section_item:
+ label_id = section_item.id or ''
+ label_text = section_item.text or ''
+ label_version = section_item.version or ''
+ os.write( fd, ' <label id="%s" text="%s" version="%s" />\n' % ( label_id, label_text, label_version ) )
+ os.write( fd, ' </section>\n' )
+ os.write( fd, '</toolbox>\n' )
+ os.close( fd )
+ shutil.move( filename, os.path.abspath( self._integrated_tool_panel_config ) )
+ os.chmod( self._integrated_tool_panel_config, 0644 )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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Branch: refs/tags/0.5
Home: https://github.com/galaxyproject/ansible-galaxy
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