1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5f6fe1916f79/
Changeset: 5f6fe1916f79
User: guerler
Date: 2015-01-15 20:01:46+00:00
Summary: ToolForm/Workflow: Show errors on refresh
Affected #: 12 files
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 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
@@ -76,6 +76,20 @@
}
},
+ /** Highlights errors
+ */
+ _errors: function(options) {
+ if (options && options.errors) {
+ var error_messages = this.tree.matchResponse(options.errors);
+ for (var input_id in this.element_list) {
+ var input = this.element_list[input_id];
+ if (error_messages[input_id]) {
+ this.highlight(input_id, error_messages[input_id], true);
+ }
+ }
+ }
+ },
+
/** Main tool form build function. This function is called once a new model is available.
*/
_buildForm: function() {
@@ -111,16 +125,11 @@
this.tree.finalize();
// show errors
- if (options.errors) {
- var error_messages = this.tree.matchResponse(options.errors);
- for (var input_id in error_messages) {
- this.highlight(input_id, error_messages[input_id], true);
- }
- }
+ this._errors(options);
// add refresh listener
this.on('refresh', function() {
- // by using/reseting the deferred ajax queue the number of redundant calls is reduced
+ // by using/resetting the deferred ajax queue the number of redundant calls is reduced
self.deferred.reset();
self.deferred.execute(function(){self._updateModel()});
});
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 client/galaxy/scripts/mvc/tools/tools-form-workflow.js
--- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js
@@ -282,7 +282,10 @@
success : function(data) {
// update node in workflow module
self.node.update_field_data(data);
-
+
+ // highlight errors
+ self._errors(data && data.tool_model);
+
// process completed
self.deferred.done(process_id);
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 client/galaxy/scripts/mvc/tools/tools-input.js
--- a/client/galaxy/scripts/mvc/tools/tools-input.js
+++ b/client/galaxy/scripts/mvc/tools/tools-input.js
@@ -51,9 +51,11 @@
/** Set error text
*/
error: function(text) {
- this.$error_text.html(text);
- this.$error.fadeIn();
- this.$el.addClass('ui-error');
+ if (!this.field.skip) {
+ this.$error_text.html(text);
+ this.$error.fadeIn();
+ this.$el.addClass('ui-error');
+ }
},
/** Reset this view
@@ -70,6 +72,7 @@
this.$field.fadeIn('fast');
this.$title_optional.html('Disable');
} else {
+ this.reset();
this.$field.hide();
this.$title_optional.html('Enable');
this.field.value && this.field.value(this.defaultvalue);
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 client/galaxy/scripts/mvc/tools/tools-tree.js
--- a/client/galaxy/scripts/mvc/tools/tools-tree.js
+++ b/client/galaxy/scripts/mvc/tools/tools-tree.js
@@ -123,7 +123,7 @@
}
// handle simple value
- if (!field.skip || self.app.workflow) {
+ if (!field.skip ) {
if (field.validate && !field.validate()) {
value = null;
}
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 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
@@ -76,6 +76,20 @@
}
},
+ /** Highlights errors
+ */
+ _errors: function(options) {
+ if (options && options.errors) {
+ var error_messages = this.tree.matchResponse(options.errors);
+ for (var input_id in this.element_list) {
+ var input = this.element_list[input_id];
+ if (error_messages[input_id]) {
+ this.highlight(input_id, error_messages[input_id], true);
+ }
+ }
+ }
+ },
+
/** Main tool form build function. This function is called once a new model is available.
*/
_buildForm: function() {
@@ -111,16 +125,11 @@
this.tree.finalize();
// show errors
- if (options.errors) {
- var error_messages = this.tree.matchResponse(options.errors);
- for (var input_id in error_messages) {
- this.highlight(input_id, error_messages[input_id], true);
- }
- }
+ this._errors(options);
// add refresh listener
this.on('refresh', function() {
- // by using/reseting the deferred ajax queue the number of redundant calls is reduced
+ // by using/resetting the deferred ajax queue the number of redundant calls is reduced
self.deferred.reset();
self.deferred.execute(function(){self._updateModel()});
});
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 static/scripts/mvc/tools/tools-form-workflow.js
--- a/static/scripts/mvc/tools/tools-form-workflow.js
+++ b/static/scripts/mvc/tools/tools-form-workflow.js
@@ -282,7 +282,10 @@
success : function(data) {
// update node in workflow module
self.node.update_field_data(data);
-
+
+ // highlight errors
+ self._errors(data && data.tool_model);
+
// process completed
self.deferred.done(process_id);
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 static/scripts/mvc/tools/tools-input.js
--- a/static/scripts/mvc/tools/tools-input.js
+++ b/static/scripts/mvc/tools/tools-input.js
@@ -51,9 +51,11 @@
/** Set error text
*/
error: function(text) {
- this.$error_text.html(text);
- this.$error.fadeIn();
- this.$el.addClass('ui-error');
+ if (!this.field.skip) {
+ this.$error_text.html(text);
+ this.$error.fadeIn();
+ this.$el.addClass('ui-error');
+ }
},
/** Reset this view
@@ -70,6 +72,7 @@
this.$field.fadeIn('fast');
this.$title_optional.html('Disable');
} else {
+ this.reset();
this.$field.hide();
this.$title_optional.html('Enable');
this.field.value && this.field.value(this.defaultvalue);
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 static/scripts/mvc/tools/tools-tree.js
--- a/static/scripts/mvc/tools/tools-tree.js
+++ b/static/scripts/mvc/tools/tools-tree.js
@@ -123,7 +123,7 @@
}
// handle simple value
- if (!field.skip || self.app.workflow) {
+ if (!field.skip ) {
if (field.validate && !field.validate()) {
value = null;
}
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 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){console.debug(l);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.options=l;this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},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){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_buildForm:function(){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);var n=this.options;this._renderForm(n);this.tree.finalize();if(n.errors){var o=this.tree.matchResponse(n.errors);for(var m in o){this.highlight(m,o[m],true)}}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var p in this.element_list){this.element_list[p].reset()}});this.trigger("refresh")},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!this.workflow&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!this.workflow&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){u.id=u.id.replace(u.version,this.version);u.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!this.workflow&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.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="+u.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/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(this.options.workflow){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})});
\ No newline at end of file
+define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){console.debug(l);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.options=l;this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_buildForm:function(){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);var m=this.options;this._renderForm(m);this.tree.finalize();this._errors(m);this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!this.workflow&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!this.workflow&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){u.id=u.id.replace(u.version,this.version);u.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!this.workflow&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(this.options.workflow){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})});
\ No newline at end of file
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 static/scripts/packed/mvc/tools/tools-form-workflow.js
--- a/static/scripts/packed/mvc/tools/tools-form-workflow.js
+++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.workflow=true;this.options=e;b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Edit Step Attributes",type:"section",expand:this.node.annotation,inputs:[{label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or notes to this step; annotations are available when a workflow is viewed.",value:this.node.annotation}]};this.post_job_actions=this.node.post_job_actions;for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:"None"});var f={label:"Edit Step Action: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"None",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"text",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."},{action:"EmailAction",label:"Email notification",type:"boolean",value:"false",ignore:"false",help:"This action will send an email notifying you when the job is done.",payload:{host:window.location.host}},{action:"DeleteIntermediatesAction",label:"Delete non-outputs",type:"boolean",value:"false",ignore:"false",help:"All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id;b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.workflow=true;this.options=e;b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Edit Step Attributes",type:"section",expand:this.node.annotation,inputs:[{label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or notes to this step; annotations are available when a workflow is viewed.",value:this.node.annotation}]};this.post_job_actions=this.node.post_job_actions;for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:"None"});var f={label:"Edit Step Action: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"None",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"text",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."},{action:"EmailAction",label:"Email notification",type:"boolean",value:"false",ignore:"false",help:"This action will send an email notifying you when the job is done.",payload:{host:window.location.host}},{action:"DeleteIntermediatesAction",label:"Delete non-outputs",type:"boolean",value:"false",ignore:"false",help:"All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id;b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}});
\ No newline at end of file
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 static/scripts/packed/mvc/tools/tools-input.js
--- a/static/scripts/packed/mvc/tools/tools-input.js
+++ b/static/scripts/packed/mvc/tools/tools-input.js
@@ -1,1 +1,1 @@
-define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.field=c.field;this.defaultvalue=c.defaultvalue;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&((this.field.validate&&!this.field.validate())||!b||(b==this.defaultvalue)||(Number(b)==Number(this.defaultvalue))||(JSON.stringify(b)==JSON.stringify(this.defaultvalue))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.$field.hide();this.$title_optional.html("Enable");this.field.value&&this.field.value(this.defaultvalue)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})});
\ No newline at end of file
+define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.field=c.field;this.defaultvalue=c.defaultvalue;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&((this.field.validate&&!this.field.validate())||!b||(b==this.defaultvalue)||(Number(b)==Number(this.defaultvalue))||(JSON.stringify(b)==JSON.stringify(this.defaultvalue))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){if(!this.field.skip){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")}},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.reset();this.$field.hide();this.$title_optional.html("Enable");this.field.value&&this.field.value(this.defaultvalue)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})});
\ No newline at end of file
diff -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f -r 5f6fe1916f79865bfb4e4fdd75d1d979139ac501 static/scripts/packed/mvc/tools/tools-tree.js
--- a/static/scripts/packed/mvc/tools/tools-tree.js
+++ b/static/scripts/packed/mvc/tools/tools-tree.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(!t.skip||b.app.workflow){if(t.validate&&!t.validate()){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})});
\ No newline at end of file
+define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(!t.skip){if(t.validate&&!t.validate()){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f7235d0ad14f/
Changeset: f7235d0ad14f
Branch: stable
User: jmchilton
Date: 2015-01-15 18:20:34+00:00
Summary: Skip extra wrapping around template-style macros.
Cheetah wants these to be strings.
Affected #: 1 file
diff -r 33cdbd98c2398f08a2d776813a8128134f90c6db -r f7235d0ad14fd90b8977e88f68715a7dedc5bab9 lib/galaxy/tools/evaluation.py
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -348,7 +348,7 @@
Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place.
"""
# chromInfo is a filename, do not sanitize it.
- skip = [ 'chromInfo' ]
+ skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys()
if not self.tool or not self.tool.options or self.tool.options.sanitize:
for key, value in param_dict.items():
if key not in skip:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/0dbf7edd5bc4/
Changeset: 0dbf7edd5bc4
User: jmchilton
Date: 2015-01-15 18:20:34+00:00
Summary: Skip extra wrapping around template-style macros.
Cheetah wants these to be strings.
Affected #: 1 file
diff -r 187f6d30c81ab194dbe1fc17b6afef707f98be8b -r 0dbf7edd5bc48857e6ad859fee2359b8abfd852f lib/galaxy/tools/evaluation.py
--- a/lib/galaxy/tools/evaluation.py
+++ b/lib/galaxy/tools/evaluation.py
@@ -382,7 +382,7 @@
Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place.
"""
# chromInfo is a filename, do not sanitize it.
- skip = [ 'chromInfo' ]
+ skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys()
if not self.tool or not self.tool.options or self.tool.options.sanitize:
for key, value in param_dict.items():
if key not in skip:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/187f6d30c81a/
Changeset: 187f6d30c81a
User: dannon
Date: 2015-01-15 17:23:33+00:00
Summary: Add six egg for John. It'll be in use soon.
Affected #: 1 file
diff -r 474e3b432da38c440491469a3f684ea9359cc443 -r 187f6d30c81ab194dbe1fc17b6afef707f98be8b eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -63,6 +63,7 @@
requests = 2.2.1
Routes = 1.12.3
simplejson = 2.1.1
+six = 1.9.0
sqlalchemy_migrate = 0.7.2
ssh = 1.7.14
SVGFig = 1.1.6
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/474e3b432da3/
Changeset: 474e3b432da3
User: dannon
Date: 2015-01-15 16:59:20+00:00
Summary: Bump bioblend to 0.5.2. The egg no longer depends on mock, which is sort of a bandaid fix for the startup eggs dependency bug not fetching it correctly. TODO: followup on that bug.
Affected #: 1 file
diff -r 0fd00352949c5d407e36f5d1ff0ffbcd699931c6 -r 474e3b432da38c440491469a3f684ea9359cc443 eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -34,7 +34,7 @@
amqp = 1.4.5
anyjson = 0.3.3
Beaker = 1.4
-bioblend = 0.4.2
+bioblend = 0.5.2
boto = 2.27.0
decorator = 3.1.2
docutils = 0.7
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/33cdbd98c239/
Changeset: 33cdbd98c239
Branch: stable
User: natefoo
Date: 2015-01-15 17:00:23+00:00
Summary: Update tag latest_2015.01.13 for changeset 3b559c4b9399
Affected #: 1 file
diff -r 3b559c4b9399236ae2a76ea1f061fcd660e76ed5 -r 33cdbd98c2398f08a2d776813a8128134f90c6db .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -22,4 +22,4 @@
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06
2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13
-2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee latest_2015.01.13
+3b559c4b9399236ae2a76ea1f061fcd660e76ed5 latest_2015.01.13
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3b559c4b9399/
Changeset: 3b559c4b9399
Branch: stable
User: dannon
Date: 2015-01-15 12:53:44+00:00
Summary: Merged in guerler/guerler-galaxy-central/stable (pull request #632)
Upload: Fix space_to_tab option
Affected #: 3 files
diff -r 5e1b2c9da932b46776e56453d1bd2acec5c89760 -r 3b559c4b9399236ae2a76ea1f061fcd660e76ed5 client/galaxy/scripts/mvc/upload/upload-view.js
--- a/client/galaxy/scripts/mvc/upload/upload-view.js
+++ b/client/galaxy/scripts/mvc/upload/upload-view.js
@@ -336,8 +336,8 @@
tool_input['dbkey'] = genome;
tool_input['file_type'] = extension;
tool_input['files_0|type'] = 'upload_dataset';
- tool_input['space_to_tabs'] = space_to_tabs;
- tool_input['to_posix_lines'] = to_posix_lines;
+ tool_input['files_0|space_to_tab'] = space_to_tabs && 'Yes' || null;
+ tool_input['files_0|to_posix_lines'] = to_posix_lines && 'Yes' || null;
// setup data
data = {};
diff -r 5e1b2c9da932b46776e56453d1bd2acec5c89760 -r 3b559c4b9399236ae2a76ea1f061fcd660e76ed5 static/scripts/mvc/upload/upload-view.js
--- a/static/scripts/mvc/upload/upload-view.js
+++ b/static/scripts/mvc/upload/upload-view.js
@@ -336,8 +336,8 @@
tool_input['dbkey'] = genome;
tool_input['file_type'] = extension;
tool_input['files_0|type'] = 'upload_dataset';
- tool_input['space_to_tabs'] = space_to_tabs;
- tool_input['to_posix_lines'] = to_posix_lines;
+ tool_input['files_0|space_to_tab'] = space_to_tabs && 'Yes' || null;
+ tool_input['files_0|to_posix_lines'] = to_posix_lines && 'Yes' || null;
// setup data
data = {};
diff -r 5e1b2c9da932b46776e56453d1bd2acec5c89760 -r 3b559c4b9399236ae2a76ea1f061fcd660e76ed5 static/scripts/packed/mvc/upload/upload-view.js
--- a/static/scripts/packed/mvc/upload/upload-view.js
+++ b/static/scripts/packed/mvc/upload/upload-view.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){j.preventDefault();h.show()}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}}});f.get({url:galaxy_config.root+"api/genomes",success:function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})}});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},show:function(){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.show()},500);return}if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(j,k,l){h._eventAnnounce(j,k,l)},initialize:function(j,k,l){return h._eventInitialize(j,k,l)},progress:function(j,k,l){h._eventProgress(j,k,l)},success:function(j,k,l){h._eventSuccess(j,k,l)},error:function(j,k,l){h._eventError(j,k,l)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
+define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){j.preventDefault();h.show()}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}}});f.get({url:galaxy_config.root+"api/genomes",success:function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})}});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},show:function(){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.show()},500);return}if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(j,k,l){h._eventAnnounce(j,k,l)},initialize:function(j,k,l){return h._eventInitialize(j,k,l)},progress:function(j,k,l){h._eventProgress(j,k,l)},success:function(j,k,l){h._eventSuccess(j,k,l)},error:function(j,k,l){h._eventError(j,k,l)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|space_to_tab"]=l&&"Yes"||null;tool_input["files_0|to_posix_lines"]=i&&"Yes"||null;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/339efd7527d2/
Changeset: 339efd7527d2
Branch: stable
User: guerler
Date: 2015-01-14 20:59:46+00:00
Summary: Upload: Fix space_to_tab option
Affected #: 3 files
diff -r fd1946912be3f0454e155effc10e5a2127388559 -r 339efd7527d21f22ace2a0f285d7221a117cd97f client/galaxy/scripts/mvc/upload/upload-view.js
--- a/client/galaxy/scripts/mvc/upload/upload-view.js
+++ b/client/galaxy/scripts/mvc/upload/upload-view.js
@@ -336,8 +336,8 @@
tool_input['dbkey'] = genome;
tool_input['file_type'] = extension;
tool_input['files_0|type'] = 'upload_dataset';
- tool_input['space_to_tabs'] = space_to_tabs;
- tool_input['to_posix_lines'] = to_posix_lines;
+ tool_input['files_0|space_to_tab'] = space_to_tabs && 'Yes' || null;
+ tool_input['files_0|to_posix_lines'] = to_posix_lines && 'Yes' || null;
// setup data
data = {};
diff -r fd1946912be3f0454e155effc10e5a2127388559 -r 339efd7527d21f22ace2a0f285d7221a117cd97f static/scripts/mvc/upload/upload-view.js
--- a/static/scripts/mvc/upload/upload-view.js
+++ b/static/scripts/mvc/upload/upload-view.js
@@ -336,8 +336,8 @@
tool_input['dbkey'] = genome;
tool_input['file_type'] = extension;
tool_input['files_0|type'] = 'upload_dataset';
- tool_input['space_to_tabs'] = space_to_tabs;
- tool_input['to_posix_lines'] = to_posix_lines;
+ tool_input['files_0|space_to_tab'] = space_to_tabs && 'Yes' || null;
+ tool_input['files_0|to_posix_lines'] = to_posix_lines && 'Yes' || null;
// setup data
data = {};
diff -r fd1946912be3f0454e155effc10e5a2127388559 -r 339efd7527d21f22ace2a0f285d7221a117cd97f static/scripts/packed/mvc/upload/upload-view.js
--- a/static/scripts/packed/mvc/upload/upload-view.js
+++ b/static/scripts/packed/mvc/upload/upload-view.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){j.preventDefault();h.show()}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}}});f.get({url:galaxy_config.root+"api/genomes",success:function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})}});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},show:function(){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.show()},500);return}if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(j,k,l){h._eventAnnounce(j,k,l)},initialize:function(j,k,l){return h._eventInitialize(j,k,l)},progress:function(j,k,l){h._eventProgress(j,k,l)},success:function(j,k,l){h._eventSuccess(j,k,l)},error:function(j,k,l){h._eventError(j,k,l)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
+define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){j.preventDefault();h.show()}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}}});f.get({url:galaxy_config.root+"api/genomes",success:function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})}});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},show:function(){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.show()},500);return}if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(j,k,l){h._eventAnnounce(j,k,l)},initialize:function(j,k,l){return h._eventInitialize(j,k,l)},progress:function(j,k,l){h._eventProgress(j,k,l)},success:function(j,k,l){h._eventSuccess(j,k,l)},error:function(j,k,l){h._eventError(j,k,l)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|space_to_tab"]=l&&"Yes"||null;tool_input["files_0|to_posix_lines"]=i&&"Yes"||null;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/3b559c4b9399/
Changeset: 3b559c4b9399
Branch: stable
User: dannon
Date: 2015-01-15 12:53:44+00:00
Summary: Merged in guerler/guerler-galaxy-central/stable (pull request #632)
Upload: Fix space_to_tab option
Affected #: 3 files
diff -r 5e1b2c9da932b46776e56453d1bd2acec5c89760 -r 3b559c4b9399236ae2a76ea1f061fcd660e76ed5 client/galaxy/scripts/mvc/upload/upload-view.js
--- a/client/galaxy/scripts/mvc/upload/upload-view.js
+++ b/client/galaxy/scripts/mvc/upload/upload-view.js
@@ -336,8 +336,8 @@
tool_input['dbkey'] = genome;
tool_input['file_type'] = extension;
tool_input['files_0|type'] = 'upload_dataset';
- tool_input['space_to_tabs'] = space_to_tabs;
- tool_input['to_posix_lines'] = to_posix_lines;
+ tool_input['files_0|space_to_tab'] = space_to_tabs && 'Yes' || null;
+ tool_input['files_0|to_posix_lines'] = to_posix_lines && 'Yes' || null;
// setup data
data = {};
diff -r 5e1b2c9da932b46776e56453d1bd2acec5c89760 -r 3b559c4b9399236ae2a76ea1f061fcd660e76ed5 static/scripts/mvc/upload/upload-view.js
--- a/static/scripts/mvc/upload/upload-view.js
+++ b/static/scripts/mvc/upload/upload-view.js
@@ -336,8 +336,8 @@
tool_input['dbkey'] = genome;
tool_input['file_type'] = extension;
tool_input['files_0|type'] = 'upload_dataset';
- tool_input['space_to_tabs'] = space_to_tabs;
- tool_input['to_posix_lines'] = to_posix_lines;
+ tool_input['files_0|space_to_tab'] = space_to_tabs && 'Yes' || null;
+ tool_input['files_0|to_posix_lines'] = to_posix_lines && 'Yes' || null;
// setup data
data = {};
diff -r 5e1b2c9da932b46776e56453d1bd2acec5c89760 -r 3b559c4b9399236ae2a76ea1f061fcd660e76ed5 static/scripts/packed/mvc/upload/upload-view.js
--- a/static/scripts/packed/mvc/upload/upload-view.js
+++ b/static/scripts/packed/mvc/upload/upload-view.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){j.preventDefault();h.show()}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}}});f.get({url:galaxy_config.root+"api/genomes",success:function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})}});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},show:function(){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.show()},500);return}if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(j,k,l){h._eventAnnounce(j,k,l)},initialize:function(j,k,l){return h._eventInitialize(j,k,l)},progress:function(j,k,l){h._eventProgress(j,k,l)},success:function(j,k,l){h._eventSuccess(j,k,l)},error:function(j,k,l){h._eventError(j,k,l)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
+define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){j.preventDefault();h.show()}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}}});f.get({url:galaxy_config.root+"api/genomes",success:function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})}});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},show:function(){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.show()},500);return}if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(j,k,l){h._eventAnnounce(j,k,l)},initialize:function(j,k,l){return h._eventInitialize(j,k,l)},progress:function(j,k,l){h._eventProgress(j,k,l)},success:function(j,k,l){h._eventSuccess(j,k,l)},error:function(j,k,l){h._eventError(j,k,l)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|space_to_tab"]=l&&"Yes"||null;tool_input["files_0|to_posix_lines"]=i&&"Yes"||null;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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