diff --git a/client/galaxy/scripts/mvc/form/form-select-content.js b/client/galaxy/scripts/mvc/form/form-select-content.js index 90aef404fc3..c3445fb017c 100644 --- a/client/galaxy/scripts/mvc/form/form-select-content.js +++ b/client/galaxy/scripts/mvc/form/form-select-content.js @@ -2,9 +2,6 @@ define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs', 'mvc/tools/tools-template'], function(Utils, Ui, Tabs, ToolTemplate) { -// track current history elements -history = {}; - // hda/hdca content selector ui element var View = Backbone.View.extend({ // initialize @@ -13,6 +10,10 @@ var View = Backbone.View.extend({ this.app = app; this.options = options; + // track current history elements + this.history = {}; + + // link this var self = this; @@ -197,7 +198,7 @@ var View = Backbone.View.extend({ value: item.id }); // backup to local history - history[item.id + '_' + item.src] = item; + self.history[item.id + '_' + item.src] = item; } // update field field.update(select_options); @@ -272,7 +273,7 @@ var View = Backbone.View.extend({ // append to dataset ids for (var i in id_list) { - var details = history[id_list[i] + '_' + this.list[this.current].type]; + var details = this.history[id_list[i] + '_' + this.list[this.current].type]; if (details) { result.values.push(details); } else { @@ -315,7 +316,7 @@ var View = Backbone.View.extend({ /** Assists in identifying the batch mode */ _batch: function() { if (this.current == 'collection') { - var hdca = history[this._select().value() + '_hdca']; + var hdca = this.history[this._select().value() + '_hdca']; if (hdca && hdca.map_over_type) { return true; } diff --git a/lib/galaxy/auth/providers/ldap_ad.py b/lib/galaxy/auth/providers/ldap_ad.py index 5053641d8cb..1db54c7ff38 100644 --- a/lib/galaxy/auth/providers/ldap_ad.py +++ b/lib/galaxy/auth/providers/ldap_ad.py @@ -125,16 +125,18 @@ class LDAP(AuthProvider): else: l.simple_bind_s() - scope = ldap.SCOPE_SUBTREE - # setup search attributes = [_.strip().format(**params) for _ in options['search-fields'].split(',')] - result = l.search(_get_subs(options, 'search-base', params), scope, - _get_subs(options, 'search-filter', params), attributes) + suser = l.search_ext_s(_get_subs(options, 'search-base', params), + ldap.SCOPE_SUBTREE, + _get_subs(options, 'search-filter', params), attributes, + timeout=60, sizelimit=1) # parse results - _, suser = l.result(result, 60) + if suser is None or len(suser) == 0: + log.warn('LDAP authenticate: search returned no results') + return (failure_mode, '', '') dn, attrs = suser[0] log.debug(("LDAP authenticate: dn is %s" % dn)) log.debug(("LDAP authenticate: search attributes are %s" % attrs)) @@ -162,8 +164,12 @@ class LDAP(AuthProvider): l.protocol_version = 3 l.simple_bind_s(_get_subs( options, 'bind-user', params), _get_subs(options, 'bind-password', params)) + whoami = l.whoami_s() + log.debug("LDAP authenticate: whoami is %s", whoami) + if whoami is None: + raise RuntimeError('LDAP authenticate: anonymous bind') except Exception: - log.exception('LDAP authenticate: bind exception') + log.warn('LDAP authenticate: bind exception', exc_info=True) return (failure_mode, '', '') log.debug('LDAP authentication successful') diff --git a/lib/galaxy/tools/parser/xml.py b/lib/galaxy/tools/parser/xml.py index 61e1005c1a8..23719e2fe94 100644 --- a/lib/galaxy/tools/parser/xml.py +++ b/lib/galaxy/tools/parser/xml.py @@ -300,6 +300,7 @@ def _test_elem_to_dict(test_elem, i): outputs=__parse_output_elems(test_elem), output_collections=__parse_output_collection_elems(test_elem), inputs=__parse_input_elems(test_elem, i), + expect_num_outputs=test_elem.get("expect_num_outputs"), command=__parse_assert_list_from_elem( test_elem.find("assert_command") ), stdout=__parse_assert_list_from_elem( test_elem.find("assert_stdout") ), stderr=__parse_assert_list_from_elem( test_elem.find("assert_stderr") ), diff --git a/static/maps/mvc/form/form-select-content.js.map b/static/maps/mvc/form/form-select-content.js.map index 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\ No newline at end of file diff --git a/static/scripts/mvc/form/form-select-content.js b/static/scripts/mvc/form/form-select-content.js index d695833fc70..b071f73ba0a 100644 --- a/static/scripts/mvc/form/form-select-content.js +++ b/static/scripts/mvc/form/form-select-content.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){history={};var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d;var e=this;this.setElement('
'),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var c=[];for(var d in b){var e=b[d];c.push({label:e.hid+": "+e.name,value:e.id}),history[e.id+"_"+e.src]=e}a.update(c)}}b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){console.debug("tools-select-content::value() - Skipped.")}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'
This is a batch mode input field. A separate job will be triggered for each dataset.
'}});return{View:c}}); +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d,this.history={};var e=this;this.setElement('
'),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var d=[];for(var e in b){var f=b[e];d.push({label:f.hid+": "+f.name,value:f.id}),c.history[f.id+"_"+f.src]=f}a.update(d)}}var c=this;b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){console.debug("tools-select-content::value() - Skipped.")}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=this.history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=this.history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'
This is a batch mode input field. A separate job will be triggered for each dataset.
'}});return{View:c}}); //# sourceMappingURL=../../../maps/mvc/form/form-select-content.js.map \ No newline at end of file