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commit/galaxy-central: jmchilton: Improvements to API import/export test case.
by commits-noreply＠bitbucket.org 25 Aug '14

25 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9d8b9171a945/ Changeset: 9d8b9171a945 User: jmchilton Date: 2014-08-25 01:37:33 Summary: Improvements to API import/export test case. Actually do some verification of imported history, eliminiate use of deprecated mixin, timeout operations that 'wait', break up big function and name test better. Affected #: 2 files diff -r 4e51563b62b5bf497ad42c53868dc9d48d39146c -r 9d8b9171a945341e36aae88572d4d37dd9b12ef2 test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -343,17 +343,27 @@ def wait_on_state( state_func, assert_ok=False, timeout=5 ): + def get_state( ): + response = state_func() + assert response.status_code == 200, "Failed to fetch state update while waiting." + state = response.json()[ "state" ] + if state not in [ "running", "queued", "new" ]: + if assert_ok: + assert state == "ok", "Final state - %s - not okay." % state + return state + else: + return None + wait_on( get_state, desc="state", timeout=timeout) + + +def wait_on( function, desc, timeout=5 ): delta = .25 iteration = 0 while True: if (delta * iteration) > timeout: - assert False, "Timed out waiting on state." + assert False, "Timed out waiting on %s." % desc iteration += 1 - response = state_func() - assert response.status_code == 200, "Failed to fetch state update while waiting." - state = response.json()[ "state" ] - if state not in [ "running", "queued", "new" ]: - break + value = function() + if value is not None: + return value time.sleep( delta ) - if assert_ok: - assert state == "ok", "Final state - %s - not okay." % state diff -r 4e51563b62b5bf497ad42c53868dc9d48d39146c -r 9d8b9171a945341e36aae88572d4d37dd9b12ef2 test/api/test_histories.py --- a/test/api/test_histories.py +++ b/test/api/test_histories.py @@ -1,13 +1,16 @@ -import time from base import api # requests.{post,put,get} or something like it if unavailable from base.interactor import post_request from base.interactor import put_request from base.interactor import get_request -from .helpers import TestsDatasets +from .helpers import DatasetPopulator, wait_on -class HistoriesApiTestCase( api.ApiTestCase, TestsDatasets ): +class HistoriesApiTestCase( api.ApiTestCase ): + + def setUp( self ): + super( HistoriesApiTestCase, self ).setUp( ) + self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) def test_create_history( self ): # Create a history. @@ -29,31 +32,18 @@ create_response = post_request( url=histories_url, data=post_data ) self._assert_status_code_is( create_response, 403 ) - def test_export( self ): - history_id = self._new_history( name="for_export" ) - self._new_dataset( history_id, content="1 2 3" ) - self._wait_for_history( history_id, assert_ok=True ) - export_url = self._api_url( "histories/%s/exports" % history_id , use_key=True ) - put_response = put_request( export_url ) - self._assert_status_code_is( put_response, 202 ) - # TODO: Break after some period of time. - while True: - put_response = put_request( export_url ) - if put_response.status_code == 202: - time.sleep( .1 ) - else: - break - self._assert_status_code_is( put_response, 200 ) - response = put_response.json() - self._assert_has_keys( response, "download_url" ) - download_path = response[ "download_url" ] + def test_import_export( self ): + history_id = self.dataset_populator.new_history( name="for_export" ) + self.dataset_populator.new_dataset( history_id, content="1 2 3" ) + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + download_path = self._export( history_id ) full_download_url = "%s%s?key=%s" % ( self.url, download_path, self.galaxy_interactor.api_key ) download_response = get_request( full_download_url ) self._assert_status_code_is( download_response, 200 ) def history_names(): history_index = self._get( "histories" ) - return map( lambda h: h[ "name" ], history_index.json() ) + return dict( map( lambda h: ( h[ "name" ], h ), history_index.json() ) ) import_name = "imported from archive: for_export" assert import_name not in history_names() @@ -62,11 +52,40 @@ import_response = self._post( "histories", data=import_data ) self._assert_status_code_is( import_response, 200 ) - found = False - while not found: - time.sleep( .1 ) - if import_name in history_names(): - found = True - assert found, "%s not in history names %s" % ( import_name, history_names() ) + + def has_history_with_name(): + histories = history_names() + return histories.get( import_name, None ) + + imported_history = wait_on( has_history_with_name, desc="import history" ) + imported_history_id = imported_history[ "id" ] + self.dataset_populator.wait_for_history( imported_history_id ) + contents_response = self._get( "histories/%s/contents" % imported_history_id ) + self._assert_status_code_is( contents_response, 200 ) + contents = contents_response.json() + assert len( contents ) == 1 + imported_content = self.dataset_populator.get_history_dataset_content( + history_id=imported_history_id, + dataset_id=contents[ 0 ][ "id" ] + ) + assert imported_content == "1 2 3\n" + + def _export(self, history_id): + export_url = self._api_url( "histories/%s/exports" % history_id, use_key=True ) + put_response = put_request( export_url ) + self._assert_status_code_is( put_response, 202 ) + + def export_ready_response(): + put_response = put_request( export_url ) + if put_response.status_code == 202: + return None + return put_response + + put_response = wait_on( export_ready_response, desc="export ready" ) + self._assert_status_code_is( put_response, 200 ) + response = put_response.json() + self._assert_has_keys( response, "download_url" ) + download_path = response[ "download_url" ] + return download_path #TODO: (CE) test_create_from_copy Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for FASTQ datasets peek/display of sequence counts.
by commits-noreply＠bitbucket.org 23 Aug '14

23 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4e51563b62b5/ Changeset: 4e51563b62b5 User: dan Date: 2014-08-21 21:52:35 Summary: Fix for FASTQ datasets peek/display of sequence counts. Affected #: 1 file diff -r 41f9ca7a24c5748f80ed19315786ba51f4cc19b5 -r 4e51563b62b5bf497ad42c53868dc9d48d39146c lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -460,6 +460,7 @@ """ Set the number of sequences and the number of data lines in dataset. + FIXME: This does not properly handle line wrapping """ if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize: dataset.metadata.data_lines = None @@ -470,22 +471,17 @@ seq_counter = 0 # blocks should be 4 lines long for line in file( dataset.file_name ): line = line.strip() - if line and line.startswith( '#' ) and not sequences: + if line and line.startswith( '#' ) and not data_lines: # We don't count comment lines for sequence data types continue + seq_counter += 1 + data_lines += 1 if line and line.startswith( '@' ): if seq_counter >= 4: # count previous block # blocks should be 4 lines long sequences += 1 seq_counter = 1 - else: - # in case quality line starts with @ - seq_counter += 1 - data_lines += 1 - else: - data_lines += 1 - seq_counter += 1 if seq_counter >= 4: # count final block sequences += 1 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: Implements conditionals
by commits-noreply＠bitbucket.org 23 Aug '14

23 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41f9ca7a24c5/ Changeset: 41f9ca7a24c5 User: guerler Date: 2014-08-22 20:32:07 Summary: ToolForm: Implements conditionals Affected #: 2 files diff -r 0c2fd93d22b796bb38687ca5489e7c57c3e14c21 -r 41f9ca7a24c5748f80ed19315786ba51f4cc19b5 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -103,8 +103,11 @@ // reset table this.table.delAll(); - // reset list - this.list = []; + // reset field list + this.field_list = {}; + + // reset sequential input definition list + this.inputs_sequential = {}; // model var data = new Backbone.Model(); @@ -115,65 +118,93 @@ } // trigger change - for (var id in this.list) { - this.list[id].trigger('change'); + for (var id in this.field_list) { + this.field_list[id].trigger('change'); } }, // add table row _add: function(inputs_def, data) { - // link this - var self = this; - + // identify field type + var type = inputs_def.type; + switch(type) { + // conditional field + case 'conditional': + // add label to input definition root + inputs_def.label = inputs_def.test_param.label; + + // add id to input definition root + inputs_def.name = inputs_def.test_param.name; + + // build options field + this._addRow('conditional', inputs_def, data); + + // add fields + for (var i in inputs_def.cases) { + var cases = inputs_def.cases[i]; + for (var j in cases.inputs) { + // add element to form + this._add(cases.inputs[j], data); + } + } + break; + + // default single element row + default: + this._addRow(type, inputs_def, data); + } + }, + + // add table row + _addRow: function(field_type, inputs_def, data) { // get id var id = inputs_def.name; // field wrapper var field = null; - console.log(inputs_def); - // create select field - var type = inputs_def.type; - switch(type) { + + // identify field type + switch(field_type) { // text input field case 'text' : - field = this.field_text(inputs_def, data); + field = this._field_text(inputs_def, data); break; // select field case 'select' : - field = this.field_select(inputs_def, data); + field = this._field_select(inputs_def, data); break; // radiobox field case 'radiobutton' : - field = this.field_radio(inputs_def, data); + field = this._field_radio(inputs_def, data); break; // dataset case 'data': - field = this.field_data(inputs_def, data); + field = this._field_data(inputs_def, data); break; // dataset column case 'data_column': - field = this.field_column(inputs_def, data); + field = this._field_column(inputs_def, data); break; // text area field case 'textarea' : - field = this.field_textarea(inputs_def, data); + field = this._field_textarea(inputs_def, data); break; - - // default - default: - field = new Ui.Input({ - id : 'field-' + id, - placeholder : inputs_def.placeholder, - type : inputs_def.type, - onchange : function() { - data.set(id, field.value()); - } - }); + + // conditional select field + case 'conditional': + field = this._field_conditional(inputs_def, data); + break; + } + + // check if field type was detected + if (!field) { + console.debug('tools-form::_addRow() : Unmatched field type (' + field_type + ').'); + return; } // set value @@ -182,8 +213,11 @@ } field.value(data.get(id)); - // add list - this.list[id] = field; + // add to field list + this.field_list[id] = field; + + // add to input definition into sequential list + this.inputs_sequential[id] = inputs_def; // combine field and info var $input = $('<div/>'); @@ -206,7 +240,7 @@ }, // text input field - field_text : function(inputs_def, data) { + _field_text : function(inputs_def, data) { var id = inputs_def.name; return new Ui.Input({ id : 'field-' + id, @@ -218,7 +252,7 @@ }, // text area - field_textarea : function(inputs_def, data) { + _field_textarea : function(inputs_def, data) { var id = inputs_def.name; return new Ui.Textarea({ id : 'field-' + id, @@ -228,8 +262,72 @@ }); }, + // conditional input field + _field_conditional : function(inputs_def, data) { + // link this + var self = this; + + // configure options fields + var options = []; + for (var i in inputs_def.test_param.options) { + var option = inputs_def.test_param.options[i]; + options.push({ + label: option[0], + value: option[1] + }); + } + + // select field + var id = inputs_def.name; + return new Ui.Select.View({ + id : 'field-' + id, + data : options, + value : data.get(id), + onchange : function(value) { + // update value + data.set(id, value); + + // recursively hide/show options + function _updateVisibility(root, show) { + // loop through all inputs + for (var i in root.inputs) { + // get input element + var element = root.inputs[i]; + + // identify element name + var element_id = element.name; + + // identify row + var element_row = self.table.get(element_id); + + // show/hide row + if (show) { + element_row.fadeIn(); + } else { + element_row.hide(); + } + + // check if its a nested conditional + if (element.type == 'conditional') { + // identify all cases + for (var j in element.cases) { + _updateVisibility(element.cases[j], show); + } + } + } + } + + // check value in order to hide/show options + for (var i in inputs_def.cases) { + var case_def = inputs_def.cases[i]; + _updateVisibility(case_def, case_def.value == value); + } + } + }); + }, + // data input field - field_data : function(inputs_def, data) { + _field_data : function(inputs_def, data) { // link this var self = this; @@ -248,12 +346,6 @@ }); } - // find referenced columns - var column_list = _.where(this.inputs, { - data_ref : id, - type : 'data_column' - }); - // select field return new Ui.Select.View({ id : 'field-' + id, @@ -263,6 +355,12 @@ // update value data.set(id, value); + // find referenced columns + var column_list = _.where(self.inputs_sequential, { + data_ref : id, + type : 'data_column' + }); + // find selected dataset var dataset = self.datasets.filter(value); @@ -291,7 +389,7 @@ // update referenced columns for (var i in column_list) { - var column_field = self.list[column_list[i].name] + var column_field = self.field_list[column_list[i].name] if (column_field) { column_field.update(columns); column_field.value(column_field.first()); @@ -306,7 +404,7 @@ }, // select field - field_column : function (inputs_def, data) { + _field_column : function (inputs_def, data) { // configure options fields var options = []; for (var i in inputs_def.options) { @@ -330,7 +428,7 @@ }, // select field - field_select : function (inputs_def, data) { + _field_select : function (inputs_def, data) { // configure options fields var options = []; for (var i in inputs_def.options) { @@ -360,7 +458,7 @@ }, // radio field - field_radio : function(inputs_def, data) { + _field_radio : function(inputs_def, data) { var id = inputs_def.name; return new Ui.RadioButton({ id : 'field-' + id, diff -r 0c2fd93d22b796bb38687ca5489e7c57c3e14c21 -r 41f9ca7a24c5748f80ed19315786ba51f4cc19b5 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-portlet","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets"],function(f,i,j,h,a,e,c,g){var d=Backbone.Model.extend({initialize:function(k){this.url=galaxy_config.root+"api/tools/"+k.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(l){var k=this;this.options=l;this.model=new d({id:l.id});this.datasets=new g({success:function(){k._initializeToolForm()}})},_initializeToolForm:function(){var k=this;this.model.fetch({success:function(){k.inputs=k.model.get("inputs");k.portlet=new f.View({icon:"fa-wrench",title:"<b>"+k.model.get("name")+"</b> "+k.model.get("description"),buttons:{execute:new j.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});k.table=new i.View();k.message=new j.Message();k.portlet.append(k.message.$el);$(k.main_el).append(k.portlet.$el);if(k.options.help!=""){$(k.main_el).append(c.help(k.options.help))}if(k.options.citations){$(k.main_el).append(c.citations());var l=new h.ToolCitationCollection();l.tool_id=k.options.id;var m=new a.CitationListView({collection:l});m.render();l.fetch()}k.setElement(k.portlet.content());k.portlet.append(k.table.$el);k.render()}})},render:function(){this.table.delAll();this.list=[];var k=new Backbone.Model();for(var l in this.inputs){this._add(this.inputs[l],k)}for(var l in this.list){this.list[l].trigger("change")}},_add:function(l,n){var k=this;var q=l.name;var o=null;console.log(l);var m=l.type;switch(m){case"text":o=this.field_text(l,n);break;case"select":o=this.field_select(l,n);break;case"radiobutton":o=this.field_radio(l,n);break;case"data":o=this.field_data(l,n);break;case"data_column":o=this.field_column(l,n);break;case"textarea":o=this.field_textarea(l,n);break;default:o=new j.Input({id:"field-"+q,placeholder:l.placeholder,type:l.type,onchange:function(){n.set(q,o.value())}})}if(!n.get(q)){n.set(q,l.value)}o.value(n.get(q));this.list[q]=o;var p=$("<div/>");p.append(o.$el);if(l.info){p.append('<div class="ui-table-form-info">'+l.info+"</div>")}this.table.add('<span class="ui-table-form-title">'+l.label+"</span>","25%");this.table.add(p);this.table.append(q);if(l.hide){this.table.get(q).hide()}},field_text:function(k,l){var m=k.name;return new j.Input({id:"field-"+m,value:l.get(m),onchange:function(n){l.set(m,n)}})},field_textarea:function(k,l){var m=k.name;return new j.Textarea({id:"field-"+m,onchange:function(){l.set(m,field.value())}})},field_data:function(n,q){var l=this;var r=n.name;var p=this.datasets.filterType();var m=[];for(var o in p){m.push({label:p[o].get("name"),value:p[o].get("id")})}var k=_.where(this.inputs,{data_ref:r,type:"data_column"});return new j.Select.View({id:"field-"+r,data:m,value:m[0].value,onchange:function(w){q.set(r,w);var y=l.datasets.filter(w);if(y&&k.length>0){console.debug("tool-form::field_data() - Selected dataset "+w+".");var x=y.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+w+".")}var v=[];for(var u in x){v.push({label:"Column: "+(parseInt(u)+1)+" ["+x[u]+"]",value:u})}for(var t in k){var s=l.list[k[t].name];if(s){s.update(v);s.value(s.first())}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+w+".")}}})},field_column:function(l,o){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var p=l.name;return new j.Select.View({id:"field-"+p,data:k,value:o.get(p),onchange:function(q){o.set(p,q)}})},field_select:function(l,p){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var o=j.Select;if(l.display=="checkboxes"){o=j.Checkbox}var q=l.name;return new o.View({id:"field-"+q,data:k,value:p.get(q),onchange:function(r){p.set(q,r)}})},field_radio:function(k,l){var m=k.name;return new j.RadioButton({id:"field-"+m,data:k.data,value:l.get(m),onchange:function(n){l.set(m,n)}})}});return{View:b}}); \ No newline at end of file +define(["mvc/ui/ui-portlet","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets"],function(f,i,j,h,a,e,c,g){var d=Backbone.Model.extend({initialize:function(k){this.url=galaxy_config.root+"api/tools/"+k.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(l){var k=this;this.options=l;this.model=new d({id:l.id});this.datasets=new g({success:function(){k._initializeToolForm()}})},_initializeToolForm:function(){var k=this;this.model.fetch({success:function(){k.inputs=k.model.get("inputs");k.portlet=new f.View({icon:"fa-wrench",title:"<b>"+k.model.get("name")+"</b> "+k.model.get("description"),buttons:{execute:new j.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});k.table=new i.View();k.message=new j.Message();k.portlet.append(k.message.$el);$(k.main_el).append(k.portlet.$el);if(k.options.help!=""){$(k.main_el).append(c.help(k.options.help))}if(k.options.citations){$(k.main_el).append(c.citations());var l=new h.ToolCitationCollection();l.tool_id=k.options.id;var m=new a.CitationListView({collection:l});m.render();l.fetch()}k.setElement(k.portlet.content());k.portlet.append(k.table.$el);k.render()}})},render:function(){this.table.delAll();this.field_list={};this.inputs_sequential={};var k=new Backbone.Model();for(var l in this.inputs){this._add(this.inputs[l],k)}for(var l in this.field_list){this.field_list[l].trigger("change")}},_add:function(l,p){var n=l.type;switch(n){case"conditional":l.label=l.test_param.label;l.name=l.test_param.name;this._addRow("conditional",l,p);for(var m in l.cases){var o=l.cases[m];for(var k in o.inputs){this._add(o.inputs[k],p)}}break;default:this._addRow(n,l,p)}},_addRow:function(n,k,l){var p=k.name;var m=null;switch(n){case"text":m=this._field_text(k,l);break;case"select":m=this._field_select(k,l);break;case"radiobutton":m=this._field_radio(k,l);break;case"data":m=this._field_data(k,l);break;case"data_column":m=this._field_column(k,l);break;case"textarea":m=this._field_textarea(k,l);break;case"conditional":m=this._field_conditional(k,l);break}if(!m){console.debug("tools-form::_addRow() : Unmatched field type ("+n+").");return}if(!l.get(p)){l.set(p,k.value)}m.value(l.get(p));this.field_list[p]=m;this.inputs_sequential[p]=k;var o=$("<div/>");o.append(m.$el);if(k.info){o.append('<div class="ui-table-form-info">'+k.info+"</div>")}this.table.add('<span class="ui-table-form-title">'+k.label+"</span>","25%");this.table.add(o);this.table.append(p);if(k.hide){this.table.get(p).hide()}},_field_text:function(k,l){var m=k.name;return new j.Input({id:"field-"+m,value:l.get(m),onchange:function(n){l.set(m,n)}})},_field_textarea:function(k,l){var m=k.name;return new j.Textarea({id:"field-"+m,onchange:function(){l.set(m,field.value())}})},_field_conditional:function(m,p){var k=this;var l=[];for(var n in m.test_param.options){var o=m.test_param.options[n];l.push({label:o[0],value:o[1]})}var q=m.name;return new j.Select.View({id:"field-"+q,data:l,value:p.get(q),onchange:function(u){p.set(q,u);function t(x,w){for(var A in x.inputs){var z=x.inputs[A];var v=z.name;var B=k.table.get(v);if(w){B.fadeIn()}else{B.hide()}if(z.type=="conditional"){for(var y in z.cases){t(z.cases[y],w)}}}}for(var s in m.cases){var r=m.cases[s];t(r,r.value==u)}}})},_field_data:function(m,p){var k=this;var q=m.name;var o=this.datasets.filterType();var l=[];for(var n in o){l.push({label:o[n].get("name"),value:o[n].get("id")})}return new j.Select.View({id:"field-"+q,data:l,value:l[0].value,onchange:function(w){p.set(q,w);var s=_.where(k.inputs_sequential,{data_ref:q,type:"data_column"});var y=k.datasets.filter(w);if(y&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+w+".");var x=y.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+w+".")}var v=[];for(var u in x){v.push({label:"Column: "+(parseInt(u)+1)+" ["+x[u]+"]",value:u})}for(var t in s){var r=k.field_list[s[t].name];if(r){r.update(v);r.value(r.first())}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+w+".")}}})},_field_column:function(l,o){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var p=l.name;return new j.Select.View({id:"field-"+p,data:k,value:o.get(p),onchange:function(q){o.set(p,q)}})},_field_select:function(l,p){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var o=j.Select;if(l.display=="checkboxes"){o=j.Checkbox}var q=l.name;return new o.View({id:"field-"+q,data:k,value:p.get(q),onchange:function(r){p.set(q,r)}})},_field_radio:function(k,l){var m=k.name;return new j.RadioButton({id:"field-"+m,data:k.data,value:l.get(m),onchange:function(n){l.set(m,n)}})}});return{View:b}}); \ 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: natefoo: Update tag latest_2014.08.11 for changeset 7e22f3579852
by commits-noreply＠bitbucket.org 22 Aug '14

22 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d86834553f0e/ Changeset: d86834553f0e Branch: stable User: natefoo Date: 2014-08-22 15:00:42 Summary: Update tag latest_2014.08.11 for changeset 7e22f3579852 Affected #: 1 file diff -r 7e22f35798522100ff03e1fdd4eced962b292360 -r d86834553f0e2d3636b3f545f61ae3250ead31e9 .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -6445c0fe761258410a17b95ad2f221a9e60fc5c7 latest_2014.08.11 +7e22f35798522100ff03e1fdd4eced962b292360 latest_2014.08.11 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: dan: Fix for FASTQ datasets peek/display of sequence counts.
by commits-noreply＠bitbucket.org 22 Aug '14

22 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7e22f3579852/ Changeset: 7e22f3579852 Branch: stable User: dan Date: 2014-08-21 21:52:35 Summary: Fix for FASTQ datasets peek/display of sequence counts. Affected #: 1 file diff -r b6c8afd2c2a1a214ef96c4ccf05aab8c8bc826f2 -r 7e22f35798522100ff03e1fdd4eced962b292360 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -460,6 +460,7 @@ """ Set the number of sequences and the number of data lines in dataset. + FIXME: This does not properly handle line wrapping """ if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize: dataset.metadata.data_lines = None @@ -470,22 +471,17 @@ seq_counter = 0 # blocks should be 4 lines long for line in file( dataset.file_name ): line = line.strip() - if line and line.startswith( '#' ) and not sequences: + if line and line.startswith( '#' ) and not data_lines: # We don't count comment lines for sequence data types continue + seq_counter += 1 + data_lines += 1 if line and line.startswith( '@' ): if seq_counter >= 4: # count previous block # blocks should be 4 lines long sequences += 1 seq_counter = 1 - else: - # in case quality line starts with @ - seq_counter += 1 - data_lines += 1 - else: - data_lines += 1 - seq_counter += 1 if seq_counter >= 4: # count final block sequences += 1 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: natefoo: Update tag latest_2014.08.11 for changeset 6445c0fe7612
by commits-noreply＠bitbucket.org 21 Aug '14

21 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b6c8afd2c2a1/ Changeset: b6c8afd2c2a1 Branch: stable User: natefoo Date: 2014-08-21 15:00:21 Summary: Update tag latest_2014.08.11 for changeset 6445c0fe7612 Affected #: 1 file diff -r 6445c0fe761258410a17b95ad2f221a9e60fc5c7 -r b6c8afd2c2a1a214ef96c4ccf05aab8c8bc826f2 .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -7748a83f33617f450b23557420c753754e54ee4d latest_2014.08.11 +6445c0fe761258410a17b95ad2f221a9e60fc5c7 latest_2014.08.11 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: 2 new changesets
by commits-noreply＠bitbucket.org 21 Aug '14

21 Aug '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/059dd17a77e0/ Changeset: 059dd17a77e0 User: natefoo Date: 2014-08-20 23:51:33 Summary: Style fixes for sample universe_wsgi.ini Affected #: 1 file diff -r 871a781a05070d5a227469c55c4249dbe6945e2d -r 059dd17a77e02c515e42b63bf50d2a9e37058b6c universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -229,9 +229,9 @@ # Citation related caching. Tool citations information maybe fetched from # external sources such as http://dx.doi.org/ by Galaxy - the following parameters # can be used to control the caching used to store this information. -#citation_cache_type=file -#citation_cache_data_dir=database/citations/data -#citation_cache_lock_dir=database/citations/lock +#citation_cache_type = file +#citation_cache_data_dir = database/citations/data +#citation_cache_lock_dir = database/citations/lock # External service types config file, defines what types of external_services configurations # are available in Galaxy. @@ -309,7 +309,7 @@ #smtp_password = None # If your SMTP server requires SSL from the beginning of the connection -# smtp_ssl= False +# smtp_ssl = False # On the user registration form, users may choose to join the mailing list. # This is the address of the list they'll be subscribed to. @@ -450,7 +450,7 @@ # The URL linked by the "Galaxy Q&A" link in the "Help" menu # The Galaxy Q&A site is under development; when the site is done, this URL # will be set and uncommented. -# qa_url = +#qa_url = # Serve static content, which must be enabled if you're not serving it via a # proxy server. These options should be self explanatory and so are not @@ -620,7 +620,7 @@ #enable_lucene_library_search = False # maxiumum file size to index for searching, in MB #fulltext_max_size = 500 -#fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger +#fulltext_noindex_filetypes = bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger # base URL of server providing search functionality using lucene #fulltext_url = http://localhost:8081 @@ -709,7 +709,7 @@ # Master key that allows many API admin actions to be used without actually # having a defined admin user in the database/config. Only set this if you need # to bootstrap Galaxy, you probably do not want to set this on public servers. -#master_api_key=changethis +#master_api_key = changethis # Enable tool tags (associating tools with tags). This has its own option # since its implementation has a few performance implications on startup for https://bitbucket.org/galaxy/galaxy-central/commits/0c2fd93d22b7/ Changeset: 0c2fd93d22b7 User: natefoo Date: 2014-08-20 23:51:49 Summary: Set defaults for static so they do not need to be explicitly defined in the Galaxy config. Affected #: 1 file diff -r 059dd17a77e02c515e42b63bf50d2a9e37058b6c -r 0c2fd93d22b796bb38687ca5489e7c57c3e14c21 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -561,12 +561,12 @@ # Send to dynamic app by default urlmap["/"] = app # Define static mappings from config - urlmap["/static"] = Static( conf.get( "static_dir" ), cache_time ) - urlmap["/images"] = Static( conf.get( "static_images_dir" ), cache_time ) - urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir" ), cache_time ) - urlmap["/static/style"] = Static( conf.get( "static_style_dir" ), cache_time ) - urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir" ), cache_time ) - urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", 'static/robots.txt'), cache_time ) + urlmap["/static"] = Static( conf.get( "static_dir", "./static/" ), cache_time ) + urlmap["/images"] = Static( conf.get( "static_images_dir", "./static/images" ), cache_time ) + urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir", "./static/scripts/" ), cache_time ) + urlmap["/static/style"] = Static( conf.get( "static_style_dir", "./static/style/blue" ), cache_time ) + urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir", "./static/favicon.ico" ), cache_time ) + urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", "./static/robots.txt" ), cache_time ) # wrap any static dirs for plugins plugin_frameworks = plugin_frameworks or [] 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: 2 new changesets
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8fbff1243ec6/ Changeset: 8fbff1243ec6 User: dannon Date: 2014-08-20 18:55:32 Summary: Swap remote user logout to actually follow galaxy internal logout procedure and then redirect. Also fix logic for user dropdown -- it was preventing users from seeing stuff that was actually available before. Affected #: 3 files diff -r 30c4d8730943a40646341e6adf3659cf9fd36985 -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -616,11 +616,14 @@ if biostar_url: # TODO: It would be better if we automatically logged this user out of biostar message += '<br>To logout of Biostar, please click <a href="%s" target="_blank">here</a>.' % ( biostar_url ) - return trans.fill_template( '/user/logout.mako', - refresh_frames=refresh_frames, - message=message, - status='done', - active_view="user" ) + if trans.app.config.use_remote_user and trans.app.config.remote_user_logout_href: + trans.response.send_redirect(trans.app.config.remote_user_logout_href) + else: + return trans.fill_template('/user/logout.mako', + refresh_frames=refresh_frames, + message=message, + status='done', + active_view="user" ) @web.expose def create( self, trans, cntrller='user', redirect_url='', refresh_frames=[], **kwd ): diff -r 30c4d8730943a40646341e6adf3659cf9fd36985 -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -289,34 +289,24 @@ title : "Logged in as " + this.options.user.email }); - // remote user - if (this.options.use_remote_user && this.options.remote_user_logout_href) - { - tab_user.add({ - title : "Logout", - content : this.options.remote_user_logout_href, - target : "_top" - }); - } else { - tab_user.add({ - title : "Preferences", - content : "user?cntrller=user", - target : "galaxy_main" - }); + tab_user.add({ + title : "Preferences", + content : "user?cntrller=user", + target : "galaxy_main" + }); - tab_user.add({ - title : "Custom Builds", - content : "user/dbkeys", - target : "galaxy_main" - }); - - tab_user.add({ - title : "Logout", - content : "user/logout", - target : "_top", - divider : true - }); - } + tab_user.add({ + title : "Custom Builds", + content : "user/dbkeys", + target : "galaxy_main" + }); + + tab_user.add({ + title : "Logout", + content : "user/logout", + target : "_top", + divider : true + }); // default tabs tab_user.add({ diff -r 30c4d8730943a40646341e6adf3659cf9fd36985 -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -19,13 +19,7 @@ %if trans.app.config.enable_openid and not trans.app.config.use_remote_user: <li><a href="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller )}">${_('Manage OpenIDs')}</a> linked to your account</li> %endif - %if trans.app.config.use_remote_user: - %if trans.app.config.remote_user_logout_href: - <li><a href="${trans.app.config.remote_user_logout_href}" target="_top">${_('Logout')}</a></li> - %endif - %else: - <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li> - %endif + <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li> %else: <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller )}">${_('Manage your information')}</a></li><li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller )}">${_('Manage your API keys')}</a></li> https://bitbucket.org/galaxy/galaxy-central/commits/871a781a0507/ Changeset: 871a781a0507 User: dannon Date: 2014-08-20 18:56:01 Summary: Strip trailing whitespace from galaxy.menu.js Affected #: 1 file diff -r 8fbff1243ec6a676ba6434600592ba0141bcafc2 -r 871a781a05070d5a227469c55c4249dbe6945e2d static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -10,10 +10,10 @@ { // options options: null, - + // link masthead class masthead: null, - + // initialize initialize: function(options) { @@ -21,7 +21,7 @@ this.masthead = options.masthead; this.create(); }, - + // default menu create: function() { @@ -149,7 +149,7 @@ content : "visualization/list", target : "_frame" }); - } + } this.masthead.append(tab_visualization); // @@ -300,14 +300,14 @@ content : "user/dbkeys", target : "galaxy_main" }); - + tab_user.add({ title : "Logout", content : "user/logout", target : "_top", divider : true }); - + // default tabs tab_user.add({ title : "Saved Histories", @@ -343,7 +343,7 @@ // add to masthead this.masthead.append(tab_user); } - + // identify active tab if (this.options.active_view) this.masthead.highlight(this.options.active_view); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Fix formatting in cloudlaunch.
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/30c4d8730943/ Changeset: 30c4d8730943 User: dannon Date: 2014-08-20 18:33:11 Summary: Fix formatting in cloudlaunch. Affected #: 1 file diff -r fb28ce36133ffcb6a167ba95003f4608b7574942 -r 30c4d8730943a40646341e6adf3659cf9fd36985 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -40,6 +40,7 @@ ("r3.8xlarge", "Memory optimized 8xLarge (32 vCPU/244GB RAM)"), ] + class CloudController(BaseUIController): """Galaxy Cloud Functions""" @@ -56,7 +57,7 @@ share_string=share_string, ami=ami, bucket_default=bucket_default, - instance_types = DEFAULT_INSTANCE_TYPES) + instance_types=DEFAULT_INSTANCE_TYPES) @web.expose def get_account_info(self, trans, key_id, secret): 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: dannon: Update instance types, slim down the options to recommended types. This will (eventually) make it to a single shared resource in bioblend that's used in cloudman + galaxy, but this change gets us in sync for now.
by commits-noreply＠bitbucket.org 20 Aug '14

20 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fb28ce36133f/ Changeset: fb28ce36133f User: dannon Date: 2014-08-20 18:22:38 Summary: Update instance types, slim down the options to recommended types. This will (eventually) make it to a single shared resource in bioblend that's used in cloudman + galaxy, but this change gets us in sync for now. Affected #: 2 files diff -r cb7713c693e73d90731489e267ca52a7b585d580 -r fb28ce36133ffcb6a167ba95003f4608b7574942 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -31,6 +31,14 @@ DEFAULT_KEYPAIR = 'cloudman_keypair' CLOUDMAN_TAG_KEY = 'galaxy:cloudman' +DEFAULT_INSTANCE_TYPES = [ + ("c3.large", "Compute optimized Large (2 vCPU/4GB RAM)"), + ("c3.2xlarge", "Compute optimized 2xLarge (8 vCPU/15GB RAM)"), + ("c3.8xlarge", "Compute optimized 8xLarge (32 vCPU/60GB RAM)"), + ("r3.large", "Memory optimized Large (2 vCPU/15GB RAM)"), + ("r3.2xlarge", "Memory optimized 2xLarge (8 vCPU/61GB RAM)"), + ("r3.8xlarge", "Memory optimized 8xLarge (32 vCPU/244GB RAM)"), +] class CloudController(BaseUIController): """Galaxy Cloud Functions""" @@ -47,7 +55,8 @@ default_keypair=DEFAULT_KEYPAIR, share_string=share_string, ami=ami, - bucket_default=bucket_default) + bucket_default=bucket_default, + instance_types = DEFAULT_INSTANCE_TYPES) @web.expose def get_account_info(self, trans, key_id, secret): diff -r cb7713c693e73d90731489e267ca52a7b585d580 -r fb28ce36133ffcb6a167ba95003f4608b7574942 templates/webapps/galaxy/cloud/index.mako --- a/templates/webapps/galaxy/cloud/index.mako +++ b/templates/webapps/galaxy/cloud/index.mako @@ -238,10 +238,9 @@ <div class="form-row"><label for="id_instance_type">Instance Type</label><select name="instance_type" id="id_instance_type"> - <option value="m1.large">Large</option> - <option value="m1.xlarge">Extra Large</option> - <option value="c3.2xlarge">Compute Optimized Double Extra Large</option> - <option value="m2.4xlarge">High-Memory Quadruple Extra Large</option> + %for (itype, description) in instance_types: + <option value="${itype}">${description}</option> + %endfor </select></div><div class="form-row"> 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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