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commit/galaxy-central: dannon: Correct usage of log.exception.
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8eb167f9214/ Changeset: f8eb167f9214 User: dannon Date: 2014-11-24 23:11:58+00:00 Summary: Correct usage of log.exception. Affected #: 1 file diff -r 6045d6e2f2da3737736cb7ec9564d49f1e7f8232 -r f8eb167f92141c345426db259914028317767973 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1150,7 +1150,7 @@ except Exception, e: status = 'error' message = 'Failed to reset password: %s' % str( e ) - log.exception( 'Unable to reset password: ' + str( e ) ) + log.exception( 'Unable to reset password.' ) elif email is not None: message = "The specified user does not exist." status = 'error' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fix xml sample file - fixes broken unit tests.
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6045d6e2f2da/ Changeset: 6045d6e2f2da User: jmchilton Date: 2014-11-24 20:23:02+00:00 Summary: Fix xml sample file - fixes broken unit tests. Affected #: 1 file diff -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 -r 6045d6e2f2da3737736cb7ec9564d49f1e7f8232 config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -205,7 +205,7 @@ Docker. --> + above options. --> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: More batch mode validation logic
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9c02b22ca58f/ Changeset: 9c02b22ca58f User: guerler Date: 2014-11-24 19:48:09+00:00 Summary: ToolForm: More batch mode validation logic Affected #: 6 files diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -145,14 +145,12 @@ } // check number of inputs - if (n > 1) { - if (batch_n === -1) { - batch_n = n; - } else { - if (batch_n !== n) { - this._foundError(input_id, 'Please make sure that you select the same number or a single input for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); - return false; - } + if (batch_n === -1) { + batch_n = n; + } else { + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); + return false; } } } diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -190,7 +190,7 @@ // prepare result dict var result = { - batch : !this.options.multiple && (this.current == 'collection' || id_list.length > 1), + batch : !this.options.multiple && this.current != 'single', values : [] } diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -145,14 +145,12 @@ } // check number of inputs - if (n > 1) { - if (batch_n === -1) { - batch_n = n; - } else { - if (batch_n !== n) { - this._foundError(input_id, 'Please make sure that you select the same number or a single input for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); - return false; - } + if (batch_n === -1) { + batch_n = n; + } else { + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); + return false; } } } diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -190,7 +190,7 @@ // prepare result dict var result = { - batch : !this.options.multiple && (this.current == 'collection' || id_list.length > 1), + batch : !this.options.multiple && this.current != 'single', values : [] } diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&e.validate&&!e.validate()){this._foundError(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(g>1){if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number or a single input for all batch mode fields. This field contains "+g+" selection(s) while a previous field contains "+m+".");return false}}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&e.validate&&!e.validate()){this._foundError(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+g+" selection(s) while a previous field contains "+m+".");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 -r 9c02b22ca58f3c59da8cbfd73678b9ac9b4e9216 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&(this.current=="collection"||j.length>1),values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: Adjust batch mode for collections
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/963fb2afb6d2/ Changeset: 963fb2afb6d2 User: guerler Date: 2014-11-24 19:31:19+00:00 Summary: ToolForm: Adjust batch mode for collections Affected #: 3 files diff -r 4efb0741cdb40f52100b36605be9b84f505c3a29 -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -190,7 +190,7 @@ // prepare result dict var result = { - batch : !this.options.multiple && id_list.length > 1, + batch : !this.options.multiple && (this.current == 'collection' || id_list.length > 1), values : [] } diff -r 4efb0741cdb40f52100b36605be9b84f505c3a29 -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -190,7 +190,7 @@ // prepare result dict var result = { - batch : !this.options.multiple && id_list.length > 1, + batch : !this.options.multiple && (this.current == 'collection' || id_list.length > 1), values : [] } diff -r 4efb0741cdb40f52100b36605be9b84f505c3a29 -r 963fb2afb6d2876e0e9f1a2b7021dce18e6ef0d4 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&j.length>1,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&(this.current=="collection"||j.length>1),values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Adjust batch mode submission
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4efb0741cdb4/ Changeset: 4efb0741cdb4 User: guerler Date: 2014-11-24 18:36:24+00:00 Summary: ToolForm: Adjust batch mode submission Affected #: 3 files diff -r 104537c5219c83b8124956f237caedeb07c7164e -r 4efb0741cdb40f52100b36605be9b84f505c3a29 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -190,7 +190,7 @@ // prepare result dict var result = { - batch : !this.options.multiple, + batch : !this.options.multiple && id_list.length > 1, values : [] } diff -r 104537c5219c83b8124956f237caedeb07c7164e -r 4efb0741cdb40f52100b36605be9b84f505c3a29 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -190,7 +190,7 @@ // prepare result dict var result = { - batch : !this.options.multiple, + batch : !this.options.multiple && id_list.length > 1, values : [] } diff -r 104537c5219c83b8124956f237caedeb07c7164e -r 4efb0741cdb40f52100b36605be9b84f505c3a29 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&j.length>1,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: add logging when password reset fails; stop retreving message form the request - we never need it
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/104537c5219c/ Changeset: 104537c5219c User: martenson Date: 2014-11-24 18:26:24+00:00 Summary: add logging when password reset fails; stop retreving message form the request - we never need it Affected #: 1 file diff -r 7d97ff9d4bef1a92adf5be7e61c5b4a3007a76fd -r 104537c5219c83b8124956f237caedeb07c7164e lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1119,22 +1119,22 @@ """Reset the user's password. Send an email with the new password.""" if trans.app.config.smtp_server is None: return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) - message = util.sanitize_text( util.restore_text( kwd.get( 'message', '' ) ) ) + message = '' status = 'done' if kwd.get( 'reset_password_button', False ): reset_user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() user = trans.get_user() if reset_user: if user and user.id != reset_user.id: - message = "You may only reset your own password" + message = "You may only reset your own password." status = 'error' else: chars = string.letters + string.digits new_pass = "" reset_password_length = getattr( trans.app.config, "reset_password_length", 15 ) - for i in range(reset_password_length): - new_pass = new_pass + random.choice(chars) - host = trans.request.host.split(':')[0] + for i in range( reset_password_length ): + new_pass = new_pass + random.choice( chars ) + host = trans.request.host.split( ':' )[ 0 ] if host == 'localhost': host = socket.getfqdn() body = 'Your password on %s has been reset to:\n\n %s\n' % ( host, new_pass ) @@ -1148,10 +1148,11 @@ trans.log_event( "User reset password: %s" % email ) message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login', noredirect='true' ) ) except Exception, e: + status = 'error' message = 'Failed to reset password: %s' % str( e ) - status = 'error' + log.exception( 'Unable to reset password: ' + str( e ) ) elif email is not None: - message = "The specified user does not exist" + message = "The specified user does not exist." status = 'error' elif email is None: email = "" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Tool test - verify that if 'batch' meta-parameter is False - matching is not attempted.
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7d97ff9d4bef/ Changeset: 7d97ff9d4bef User: jmchilton Date: 2014-11-24 18:02:18+00:00 Summary: Tool test - verify that if 'batch' meta-parameter is False - matching is not attempted. Affected #: 1 file diff -r 7b7dd8f82126b3c18e9d311305edae85adeea659 -r 7d97ff9d4bef1a92adf5be7e61c5b4a3007a76fd test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -273,6 +273,15 @@ self._check_repeat_multirun( history_id, inputs ) @skip_without_tool( "cat1" ) + def test_multirun_in_repeat_mismatch( self ): + history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun( ) + inputs = { + "input1": {'batch': False, 'values': [ common_dataset ] }, + 'queries_0|input2': { 'batch': True, 'values': repeat_datasets }, + } + self._check_repeat_multirun( history_id, inputs ) + + @skip_without_tool( "cat1" ) def test_multirun_on_multiple_inputs_legacy( self ): history_id, first_two, second_two = self._setup_two_multiruns() inputs = { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Tool API test for mixing batch and non-batch input datasets.
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b7dd8f82126/ Changeset: 7b7dd8f82126 User: jmchilton Date: 2014-11-24 17:56:05+00:00 Summary: Tool API test for mixing batch and non-batch input datasets. Affected #: 1 file diff -r 6cc3b0c515bce43786031f750bf4bd98d7fc9fed -r 7b7dd8f82126b3c18e9d311305edae85adeea659 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -255,26 +255,22 @@ assert sorted( map( lambda c: len( c.split( "\n" ) ), outputs_contents ) ) == [ 1, 2, 3 ] @skip_without_tool( "cat1" ) + def test_multirun_in_repeat_legacy( self ): + history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun( ) + inputs = { + "input1": common_dataset, + 'queries_0|input2|__multirun__': repeat_datasets, + } + self._check_repeat_multirun( history_id, inputs ) + + @skip_without_tool( "cat1" ) def test_multirun_in_repeat( self ): - history_id = self.dataset_populator.new_history() - new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' ) - new_dataset2 = self.dataset_populator.new_dataset( history_id, content='456' ) - common_dataset = self.dataset_populator.new_dataset( history_id, content='Common' ) + history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun( ) inputs = { - "input1": dataset_to_param( common_dataset ), - 'queries_0|input2|__multirun__': [ - dataset_to_param( new_dataset1 ), - dataset_to_param( new_dataset2 ), - ], + "input1": common_dataset, + 'queries_0|input2': { 'batch': True, 'values': repeat_datasets }, } - outputs = self._cat1_outputs( history_id, inputs=inputs ) - self.assertEquals( len( outputs ), 2 ) - output1 = outputs[ 0 ] - output2 = outputs[ 1 ] - output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 ) - output2_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output2 ) - self.assertEquals( output1_content.strip(), "Common\n123" ) - self.assertEquals( output2_content.strip(), "Common\n456" ) + self._check_repeat_multirun( history_id, inputs ) @skip_without_tool( "cat1" ) def test_multirun_on_multiple_inputs_legacy( self ): @@ -317,6 +313,27 @@ assert "123\n0ab" in outputs_contents assert "456\n789" in outputs_contents + def _setup_repeat_multirun( self ): + history_id = self.dataset_populator.new_history() + new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' ) + new_dataset2 = self.dataset_populator.new_dataset( history_id, content='456' ) + common_dataset = self.dataset_populator.new_dataset( history_id, content='Common' ) + return ( + history_id, + dataset_to_param( common_dataset ), + [ dataset_to_param( new_dataset1 ), dataset_to_param( new_dataset2 ) ] + ) + + def _check_repeat_multirun( self, history_id, inputs ): + outputs = self._cat1_outputs( history_id, inputs=inputs ) + self.assertEquals( len( outputs ), 2 ) + output1 = outputs[ 0 ] + output2 = outputs[ 1 ] + output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 ) + output2_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output2 ) + self.assertEquals( output1_content.strip(), "Common\n123" ) + self.assertEquals( output2_content.strip(), "Common\n456" ) + def _setup_two_multiruns( self ): history_id = self.dataset_populator.new_history() new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: Allow 1 to n selection for batch mode fields
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6cc3b0c515bc/ Changeset: 6cc3b0c515bc User: guerler Date: 2014-11-24 17:30:29+00:00 Summary: ToolForm: Allow 1 to n selection for batch mode fields Affected #: 3 files diff -r ebceda0721f3f3215447c19f94525f06f164afd1 -r 6cc3b0c515bce43786031f750bf4bd98d7fc9fed client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -145,12 +145,14 @@ } // check number of inputs - if (batch_n === -1) { - batch_n = n; - } else { - if (batch_n !== n) { - this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); - return false; + if (n > 1) { + if (batch_n === -1) { + batch_n = n; + } else { + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number or a single input for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); + return false; + } } } } diff -r ebceda0721f3f3215447c19f94525f06f164afd1 -r 6cc3b0c515bce43786031f750bf4bd98d7fc9fed static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -145,12 +145,14 @@ } // check number of inputs - if (batch_n === -1) { - batch_n = n; - } else { - if (batch_n !== n) { - this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); - return false; + if (n > 1) { + if (batch_n === -1) { + batch_n = n; + } else { + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number or a single input for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.'); + return false; + } } } } diff -r ebceda0721f3f3215447c19f94525f06f164afd1 -r 6cc3b0c515bce43786031f750bf4bd98d7fc9fed static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&e.validate&&!e.validate()){this._foundError(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+g+" selection(s) while a previous field contains "+m+".");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(!l||!j||!e){console.debug("tools-jobs::_validation - Retrieving input objects failed.");continue}if(!j.optional&&e.validate&&!e.validate()){this._foundError(l);return false}if(f&&f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(g>1){if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number or a single input for all batch mode fields. This field contains "+g+" selection(s) while a previous field contains "+m+".");return false}}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Allow passing extra parameter to docker run command in job_conf.xml.
by commits-noreply＠bitbucket.org 24 Nov '14

24 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ebceda0721f3/ Changeset: ebceda0721f3 User: jmchilton Date: 2014-11-24 17:24:21+00:00 Summary: Allow passing extra parameter to docker run command in job_conf.xml. As request in the following thread http://dev.list.galaxyproject.org/more-control-over-the-quot-docker-quot-co…. Affected #: 3 files diff -r 3edc85f4761bbcde996470590cc002828ce21d03 -r ebceda0721f3f3215447c19f94525f06f164afd1 config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -204,6 +204,9 @@ remote job user. Leave empty to not use the -u argument with Docker. --> +  + <!-- Following can be used to connect to docke server in different diff -r 3edc85f4761bbcde996470590cc002828ce21d03 -r ebceda0721f3f3215447c19f94525f06f164afd1 lib/galaxy/tools/deps/containers.py --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -245,6 +245,7 @@ net=prop("net", "none"), # By default, docker instance has networking disabled auto_rm=asbool(prop("auto_rm", docker_util.DEFAULT_AUTO_REMOVE)), set_user=prop("set_user", docker_util.DEFAULT_SET_USER), + run_extra_arguments=prop("run_extra_arguments", docker_util.DEFAULT_RUN_EXTRA_ARGUMENTS), **docker_host_props ) return "%s\n%s" % (cache_command, run_command) diff -r 3edc85f4761bbcde996470590cc002828ce21d03 -r ebceda0721f3f3215447c19f94525f06f164afd1 lib/galaxy/tools/deps/docker_util.py --- a/lib/galaxy/tools/deps/docker_util.py +++ b/lib/galaxy/tools/deps/docker_util.py @@ -11,6 +11,7 @@ DEFAULT_VOLUMES_FROM = None DEFAULT_AUTO_REMOVE = True DEFAULT_SET_USER = "$UID" +DEFAULT_RUN_EXTRA_ARGUMENTS = None class DockerVolume(object): @@ -116,6 +117,7 @@ working_directory=DEFAULT_WORKING_DIRECTORY, name=None, net=DEFAULT_NET, + run_extra_arguments=DEFAULT_RUN_EXTRA_ARGUMENTS, docker_cmd=DEFAULT_DOCKER_COMMAND, sudo=DEFAULT_SUDO, sudo_cmd=DEFAULT_SUDO_COMMAND, @@ -148,6 +150,8 @@ command_parts.extend(["--net", net]) if auto_rm: command_parts.append("--rm") + if run_extra_arguments: + command_parts.append(run_extra_arguments) if set_user: user = set_user if set_user == DEFAULT_SET_USER: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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