April 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: natefoo: Make the new tabular column_names metadata element optional.
by Bitbucket 17 Apr '12

17 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7e8ed93ae248/ changeset: 7e8ed93ae248 user: natefoo date: 2012-04-17 19:07:03 summary: Make the new tabular column_names metadata element optional. affected #: 1 file diff -r 564bbbdd8a223a0709420f7feb47e5fccb40a139 -r 7e8ed93ae2485f7a612d967d60d290fedddbf2b8 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -25,7 +25,7 @@ MetadataElement( name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0 ) MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False, no_value=0 ) MetadataElement( name="column_types", default=[], desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[] ) - MetadataElement( name="column_names", default=[], desc="Column names", readonly=True, visible=False, no_value=[] ) + MetadataElement( name="column_names", default=[], desc="Column names", readonly=True, visible=False, optional=True, no_value=[] ) def init_meta( self, dataset, copy_from=None ): data.Text.init_meta( self, dataset, copy_from=copy_from ) @@ -180,7 +180,13 @@ out = "Can't create peek %s" % str( exc ) return out - def make_html_peek_header( self, dataset, skipchars=[], column_names=[], column_number_format='%s', column_parameter_alias={}, **kwargs ): + def make_html_peek_header( self, dataset, skipchars=None, column_names=None, column_number_format='%s', column_parameter_alias=None, **kwargs ): + if skipchars is None: + skipchars = [] + if column_names is None: + column_names = [] + if column_parameter_alias is None: + column_parameter_alias = {} out = [] try: if not column_names and dataset.metadata.column_names: @@ -216,7 +222,9 @@ raise Exception, "Can't create peek header %s" % str( exc ) return "".join( out ) - def make_html_peek_rows( self, dataset, skipchars=[], **kwargs ): + def make_html_peek_rows( self, dataset, skipchars=None, **kwargs ): + if skipchars is None: + skipchars = [] out = [] try: if not dataset.peek: @@ -504,8 +512,10 @@ 'POSITION', 'STRAND', 'DESC', 'SRAS', 'PRAS', 'PART_CHROM' 'PART_CONTIG', 'PART_OFFSET', 'PART_STRAND', 'FILT' ] - def make_html_table( self, dataset, skipchars=[] ): + def make_html_table( self, dataset, skipchars=None ): """Create HTML table, used for displaying peek""" + if skipchars is None: + skipchars = [] out = ['<table cellspacing="0" cellpadding="3">'] try: # Generate column header Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Tool shed repository metadata fixes.
by Bitbucket 17 Apr '12

17 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/564bbbdd8a22/ changeset: 564bbbdd8a22 user: greg date: 2012-04-17 18:16:36 summary: Tool shed repository metadata fixes. affected #: 3 files diff -r 7a9f3f0c7c010db0859f0c18f3244a6b77f3bf10 -r 564bbbdd8a223a0709420f7feb47e5fccb40a139 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -462,10 +462,22 @@ tool_tests = [] if tool.tests: for ttb in tool.tests: + required_files = [] + for required_file in ttb.required_files: + value, extra = required_file + required_files.append( ( value ) ) + inputs = [] + for input in ttb.inputs: + name, value, extra = input + inputs.append( ( name, value ) ) + outputs = [] + for output in ttb.outputs: + name, file_name, extra = output + outputs.append( ( name, os.path.split( file_name )[ 1 ] ) ) test_dict = dict( name=ttb.name, - required_files=ttb.required_files, - inputs=ttb.inputs, - outputs=ttb.outputs ) + required_files=required_files, + inputs=inputs, + outputs=outputs ) tool_tests.append( test_dict ) tool_dict = dict( id=tool.id, guid=guid, diff -r 7a9f3f0c7c010db0859f0c18f3244a6b77f3bf10 -r 564bbbdd8a223a0709420f7feb47e5fccb40a139 templates/admin/tool_shed_repository/view_tool_metadata.mako --- a/templates/admin/tool_shed_repository/view_tool_metadata.mako +++ b/templates/admin/tool_shed_repository/view_tool_metadata.mako @@ -143,7 +143,7 @@ </td><td> %for required_file in required_files: - ${required_file[0]} + ${required_file} %endfor </td></tr> diff -r 7a9f3f0c7c010db0859f0c18f3244a6b77f3bf10 -r 564bbbdd8a223a0709420f7feb47e5fccb40a139 templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -254,7 +254,7 @@ </td><td> %for required_file in required_files: - ${required_file[0]} + ${required_file} %endfor </td></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Add skeleton for datasets API controller.
by Bitbucket 17 Apr '12

17 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7a9f3f0c7c01/ changeset: 7a9f3f0c7c01 user: jgoecks date: 2012-04-17 17:20:48 summary: Add skeleton for datasets API controller. affected #: 2 files diff -r 4afec5f8e54ae1ed72bea926bba901d326da10ef -r 7a9f3f0c7c010db0859f0c18f3244a6b77f3bf10 lib/galaxy/web/api/datasets.py --- /dev/null +++ b/lib/galaxy/web/api/datasets.py @@ -0,0 +1,44 @@ +""" +API operations on the contents of a dataset. +""" +import logging, os, string, shutil, urllib, re, socket +from cgi import escape, FieldStorage +from galaxy import util, datatypes, jobs, web, util +from galaxy.web.base.controller import * +from galaxy.util.sanitize_html import sanitize_html +from galaxy.model.orm import * + +log = logging.getLogger( __name__ ) + +class DatasetsController( BaseAPIController, UsesHistoryDatasetAssociation ): + + @web.expose_api + def index( self, trans, hda_id, **kwd ): + """ + GET /api/datasets + Lists datasets. + """ + pass + + @web.expose_api + def show( self, trans, id, deleted='False', **kwd ): + """ + GET /api/datasets/{encoded_dataset_id} + Displays information about and/or content of a dataset. + """ + + # Get HDA. + try: + hda = self.get_dataset( trans, id, check_ownership=True, check_accessible=True ) + except Exception, e: + return str( e ) + + # Return information about HDA. + rval = None + try: + rval = hda.get_api_value() + except Exception, e: + rval = "Error in dataset API at listing contents" + log.error( rval + ": %s" % str(e) ) + trans.response.status = 500 + return rval diff -r 4afec5f8e54ae1ed72bea926bba901d326da10ef -r 7a9f3f0c7c010db0859f0c18f3244a6b77f3bf10 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -122,6 +122,7 @@ 'permissions', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.api_mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' ) webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix for handling proprietary datatypes included in a tool shed repository being installed.
by Bitbucket 17 Apr '12

17 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4afec5f8e54a/ changeset: 4afec5f8e54a user: greg date: 2012-04-17 17:04:45 summary: Fix for handling proprietary datatypes included in a tool shed repository being installed. affected #: 1 file diff -r a09c2e0406c471fc31f18f5f7cce49e1b4b92718 -r 4afec5f8e54ae1ed72bea926bba901d326da10ef lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -214,11 +214,14 @@ elem.attrib[ 'proprietary_datatype_module' ] = proprietary_datatype_module sniffers = datatypes_config_root.find( 'sniffers' ) + else: + sniffers = None fd, proprietary_datatypes_config = tempfile.mkstemp() os.write( fd, '<?xml version="1.0"?>\n' ) os.write( fd, '<datatypes>\n' ) os.write( fd, '%s' % util.xml_to_string( registration ) ) - os.write( fd, '%s' % util.xml_to_string( sniffers ) ) + if sniffers: + os.write( fd, '%s' % util.xml_to_string( sniffers ) ) os.write( fd, '</datatypes>\n' ) os.close( fd ) os.chmod( proprietary_datatypes_config, 0644 ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Allow BCF files to be uploaded.
by Bitbucket 17 Apr '12

17 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a09c2e0406c4/ changeset: a09c2e0406c4 user: dan date: 2012-04-17 15:47:25 summary: Allow BCF files to be uploaded. affected #: 1 file diff -r ddc66d9905cc6bea0e10967013bc18737f0d10c7 -r a09c2e0406c471fc31f18f5f7cce49e1b4b92718 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -170,7 +170,7 @@ <display file="igv/vcf.xml" /><display file="rviewer/vcf.xml" inherit="True"/></datatype> - <datatype extension="bcf" type="galaxy.datatypes.binary:Binary" subclass="True"/> + <datatype extension="bcf" type="galaxy.datatypes.binary:Binary" subclass="True" display_in_upload="True"/><datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/><datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"><converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/> 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: jgoecks: Do not use template for tool panel label as it is overkill.
by Bitbucket 16 Apr '12

16 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ddc66d9905cc/ changeset: ddc66d9905cc user: jgoecks date: 2012-04-17 03:49:05 summary: Do not use template for tool panel label as it is overkill. affected #: 5 files diff -r 3cc5e3c84194b86e288beb823600237864263c79 -r ddc66d9905cc6bea0e10967013bc18737f0d10c7 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -310,12 +310,11 @@ var ToolPanelLabelView = BaseView.extend({ tagName: 'div', className: 'toolPanelLabel', - template: Handlebars.templates.panel_label, render: function() { - this.$el.append( this.template(this.model.toJSON()) ); + this.$el.append( $("").text(this.model.attributes.name) ); return this; - }, + } }); /** diff -r 3cc5e3c84194b86e288beb823600237864263c79 -r ddc66d9905cc6bea0e10967013bc18737f0d10c7 static/scripts/packed/mvc/tools.js --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:"ToolInput",reverseRelation:{key:"tool"}}],urlRoot:galaxy_paths.attributes.root_path+"api/tools",apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolInput=Backbone.RelationalModel.extend({initialize:function(){this.attributes.html=unescape(this.attributes.html)}});var ToolCollection=Backbone.Collection.extend({model:Tool});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",tools:new ToolCollection(),parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var a=this;a.tools=new ToolCollection();this.each(function(b){if(b instanceof ToolPanelSection){_.each(b.attributes.elems,function(c){if(c instanceof Tool){a.tools.push(c)}})}else{if(b instanceof Tool){a.tools.push(b)}}})},clear_search_results:function(){this.each(function(a){if(a instanceof ToolPanelSection){a.clear_search_results()}else{a.show()}})},apply_search_results:function(){var b=this.tool_search.attributes.results;if(b===null){this.clear_search_results();return}var a=null;this.each(function(c){if(c instanceof ToolPanelLabel){a=c;a.hide()}else{if(c instanceof Tool){if(c.apply_search_results(b)){if(a){a.show()}}}else{a=null;c.apply_search_results(b)}}})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var a=this;var b=new ToolSearchView({model:this.collection.tool_search});b.render();a.$el.append(b.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();a.$el.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();a.$el.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();a.$el.append(f.$el)}}}});a.$el.find("a.tool-link").click(function(f){var d=$(this).attr("class").split(/\s+/)[0],c=a.collection.tools.get(d);a.trigger("tool_link_click",f,c)});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var ToolFormView=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var IntegratedToolMenuAndView=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new ToolPanelView({collection:this.collection});this.tool_form_view=new ToolFormView()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(c,b){c.preventDefault();a.show_tool(b)})},show_tool:function(b){var a=this;b.fetch().done(function(){a.tool_form_view.model=b;a.tool_form_view.render();a.tool_form_view.$el.show();$("#left").width("650px")})}}); \ No newline at end of file +var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:"ToolInput",reverseRelation:{key:"tool"}}],urlRoot:galaxy_paths.attributes.root_path+"api/tools",apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolInput=Backbone.RelationalModel.extend({initialize:function(){this.attributes.html=unescape(this.attributes.html)}});var ToolCollection=Backbone.Collection.extend({model:Tool});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",tools:new ToolCollection(),parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var a=this;a.tools=new ToolCollection();this.each(function(b){if(b instanceof ToolPanelSection){_.each(b.attributes.elems,function(c){if(c instanceof Tool){a.tools.push(c)}})}else{if(b instanceof Tool){a.tools.push(b)}}})},clear_search_results:function(){this.each(function(a){if(a instanceof ToolPanelSection){a.clear_search_results()}else{a.show()}})},apply_search_results:function(){var b=this.tool_search.attributes.results;if(b===null){this.clear_search_results();return}var a=null;this.each(function(c){if(c instanceof ToolPanelLabel){a=c;a.hide()}else{if(c instanceof Tool){if(c.apply_search_results(b)){if(a){a.show()}}}else{a=null;c.apply_search_results(b)}}})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("").text(this.model.attributes.name));return this}});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var a=this;var b=new ToolSearchView({model:this.collection.tool_search});b.render();a.$el.append(b.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();a.$el.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();a.$el.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();a.$el.append(f.$el)}}}});a.$el.find("a.tool-link").click(function(f){var d=$(this).attr("class").split(/\s+/)[0],c=a.collection.tools.get(d);a.trigger("tool_link_click",f,c)});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var ToolFormView=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var IntegratedToolMenuAndView=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new ToolPanelView({collection:this.collection});this.tool_form_view=new ToolFormView()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(c,b){c.preventDefault();a.show_tool(b)})},show_tool:function(b){var a=this;b.fetch().done(function(){a.tool_form_view.model=b;a.tool_form_view.render();a.tool_form_view.$el.show();$("#left").width("650px")})}}); \ No newline at end of file diff -r 3cc5e3c84194b86e288beb823600237864263c79 -r ddc66d9905cc6bea0e10967013bc18737f0d10c7 static/scripts/templates/compiled/panel_label.js --- a/static/scripts/templates/compiled/panel_label.js +++ /dev/null @@ -1,15 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['panel_label'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; - - - buffer += ""; - foundHelper = helpers.name; - stack1 = foundHelper || depth0.name; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } - buffer += escapeExpression(stack1) + ""; - return buffer;}); -})(); \ No newline at end of file diff -r 3cc5e3c84194b86e288beb823600237864263c79 -r ddc66d9905cc6bea0e10967013bc18737f0d10c7 static/scripts/templates/panel_label.handlebars --- a/static/scripts/templates/panel_label.handlebars +++ /dev/null @@ -1,1 +0,0 @@ -{{name}} \ No newline at end of file diff -r 3cc5e3c84194b86e288beb823600237864263c79 -r ddc66d9905cc6bea0e10967013bc18737f0d10c7 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -16,7 +16,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.templates( "tool_link", "panel_label", "panel_section", "tool_search" )} + ${h.templates( "tool_link", "panel_section", "tool_search" )} ${h.js( "galaxy.base", "json2", "autocomplete_tagging", "mvc/tools" )} <% Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a 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commit/galaxy-central: dannon: Significantly improve handling of SAM rendering with the new tabular display. Optional parameters are accounted for now.
by Bitbucket 16 Apr '12

16 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3cc5e3c84194/ changeset: 3cc5e3c84194 user: dannon date: 2012-04-17 03:08:41 summary: Significantly improve handling of SAM rendering with the new tabular display. Optional parameters are accounted for now. For all tabular display: numerical columns align right, text aligns left. Build CSS. affected #: 4 files diff -r fa3c59a4a56cb7965c05d073dc37e3a2504a9c54 -r 3cc5e3c84194b86e288beb823600237864263c79 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1722,6 +1722,10 @@ padding:2px 10px; } +#content_table td.stringalign{ + text-align:left; +} + // ==== Integrated tool form styles .toolMenuAndView .toolForm diff -r fa3c59a4a56cb7965c05d073dc37e3a2504a9c54 -r 3cc5e3c84194b86e288beb823600237864263c79 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -726,6 +726,7 @@ #tool-search{padding-top:5px;padding-bottom:10px;position:relative;} #loading_indicator{position:fixed;right:10px;top:10px;height:32px;width:32px;background:url(largespinner.gif);} #content_table td{text-align:right;white-space:nowrap;padding:2px 10px;} +#content_table td.stringalign{text-align:left;} .toolMenuAndView .toolForm{float:left;background-color:white;margin:10px;} .icon-button.display{background:url(history-buttons.png) no-repeat 0px 0px;} .icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} diff -r fa3c59a4a56cb7965c05d073dc37e3a2504a9c54 -r 3cc5e3c84194b86e288beb823600237864263c79 static/june_2007_style/blue/library.css --- a/static/june_2007_style/blue/library.css +++ b/static/june_2007_style/blue/library.css @@ -1,9 +1,9 @@ .libraryRow{background-color:#ebd9b2;} -.datasetHighlighted{background-color:#C1C9E5;} +.datasetHighlighted{background-color:#DFE5F9;} .libraryItemDeleted-True{font-style:italic;} div.libraryItemBody{padding:4px 4px 2px 4px;} li.folderRow,li.datasetRow{border-top:solid 1px #ddd;} -li.folderRow:hover,li.datasetRow:hover{background-color:#C1C9E5;} +li.folderRow:hover,li.datasetRow:hover{background-color:#DFE5F9;} img.expanderIcon{padding-right:4px;} input.datasetCheckbox,li,ul{padding:0;margin:0;} .rowTitle{padding:2px;} diff -r fa3c59a4a56cb7965c05d073dc37e3a2504a9c54 -r 3cc5e3c84194b86e288beb823600237864263c79 templates/dataset/tabular_chunked.mako --- a/templates/dataset/tabular_chunked.mako +++ b/templates/dataset/tabular_chunked.mako @@ -6,26 +6,65 @@ <%def name="javascripts()"> ${parent.javascripts()} <script type="text/javascript"> - var DATASET_URL = "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}"; - var DATASET_COLS = ${dataset.metadata.columns}; + + var DATASET_URL = "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}"; + var DATASET_COLS = ${dataset.metadata.columns}; + var DATASET_TYPES = ${dataset.metadata.column_types}; + var current_chunk = 0; + function renderCell(cell_contents, index, colspan){ + if (colspan !== undefined){ + return '<td colspan="'+ colspan + '" class="stringalign">' + cell_contents + '</td>'; + } + else if (DATASET_TYPES[index] == 'str'){ + /* Left align all str columns, right align the rest */ + return '<td class="stringalign">'+ cell_contents + '</td>'; + } + else{ + return '<td>'+ cell_contents + '</td>'; + } + } + + function renderRow(line){ + /* Check length of cells to ensure this is a complete row. */ + var cells = line.split('\t'); + var rowstr = '<tr>'; + if (cells.length == DATASET_COLS){ + $.each(cells, function(index, cell_contents){ + rowstr += renderCell(cell_contents, index); + }); + } + else if(cells.length > DATASET_COLS){ + /* SAM file or like format with optional metadata included */ + $.each(cells.slice(0, DATASET_COLS -1), function(index, cell_contents){ + rowstr += renderCell(cell_contents, index); + }); + rowstr += renderCell(cells.slice(DATASET_COLS -1).join('\t'), DATASET_COLS-1); + } + else if(DATASET_COLS > 5 && cells.length == DATASET_COLS - 1 ){ + /* SAM file or like format with optional metadata missing */ + $.each(cells, function(index, cell_contents){ + rowstr += renderCell(cell_contents, index); + }); + rowstr += '<td></td>'; + } + else{ + /* Comment line, just return the one cell*/ + rowstr += renderCell(line, 0, DATASET_COLS); + } + rowstr += '</tr>'; + return rowstr; + } + function fillTable(){ if (current_chunk !== -1){ var table = $('#content_table'); $.getJSON(DATASET_URL, {chunk: current_chunk}, function (result) { if (result.ck_data !== ""){ var lines = result.ck_data.split('\n'); - $.each(lines, function(){ - var line = this; - var cells = line.split('\t'); - /* Check length of cells to ensure this is a complete row. */ - if (cells.length == DATASET_COLS){ - table.append('<tr><td>' + cells.join('</td><td>') + '</td></tr>'); - } - else{ - table.append('<tr><td colspan="'+ DATASET_COLS+ '">' + line + '</td></tr>'); - } + $.each(lines, function(index, line){ + table.append(renderRow(line)); }); current_chunk = result.ck_index; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Allow for starting/stopping multiple servers directly in run.sh.
by Bitbucket 16 Apr '12

16 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fa3c59a4a56c/ changeset: fa3c59a4a56c user: natefoo date: 2012-04-16 22:26:10 summary: Allow for starting/stopping multiple servers directly in run.sh. affected #: 1 file diff -r 39200ca2e42dbc4ff264f9c9708795084fbb5092 -r fa3c59a4a56cb7965c05d073dc37e3a2504a9c54 run.sh --- a/run.sh +++ b/run.sh @@ -52,4 +52,17 @@ fi fi -python ./scripts/paster.py serve universe_wsgi.ini $@ +if [ -n "$GALAXY_RUN_ALL" ]; then + servers=`sed -n 's/^\[server:$.*$\]/\1/ p' universe_wsgi.ini | xargs echo` + daemon=`echo "$@" | grep -q daemon` + if [ $? -ne 0 ]; then + echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon` or `--stop-daemon` arguments to run.sh' + exit 1 + fi + for server in $servers; do + echo "Handling $server with log file $server.log..." + python ./scripts/paster.py serve universe_wsgi.ini --server-name=$server --pid-file=$server.pid --log-file=$server.log $@ + done +else + python ./scripts/paster.py serve universe_wsgi.ini $@ +fi 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: greg: Attempt to correctly render dynamically generated select lists when previewing a tool in the tool shed.
by Bitbucket 16 Apr '12

16 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/39200ca2e42d/ changeset: 39200ca2e42d user: greg date: 2012-04-16 22:08:39 summary: Attempt to correctly render dynamically generated select lists when previewing a tool in the tool shed. affected #: 1 file diff -r 5c93ac32ace1b7f61f6c95bba0a0fe04d6f85755 -r 39200ca2e42dbc4ff264f9c9708795084fbb5092 templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -90,6 +90,16 @@ field = SelectField( param.name, display=param.display ) field.add_option( param.data_ref, param.data_ref ) field_html = field.get_html( prefix ) + elif isinstance( param, SelectToolParameter ) and param.is_dynamic: + field = SelectField( param.name, display=param.display ) + dynamic_options = param.options + if dynamic_options.index_file: + option_label = "Dynamically generated from entries in file %s" % str( dynamic_options.index_file ) + field.add_option( option_label, "none" ) + elif dynamic_options.missing_index_file: + option_label = "Dynamically generated from entries in missing file %s" % str( dynamic_options.missing_index_file ) + field.add_option( option_label, "none" ) + field_html = field.get_html( prefix ) else: field = param.get_html_field( trans, None, other_values ) field_html = field.get_html( prefix ) 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: Fix job manager/handler shutdown, functional tests due to referer -> redirect rename, and check_galaxy script for dataset display -> html table change.
by Bitbucket 16 Apr '12

16 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5c93ac32ace1/ changeset: 5c93ac32ace1 user: natefoo date: 2012-04-16 20:56:24 summary: Fix job manager/handler shutdown, functional tests due to referer -> redirect rename, and check_galaxy script for dataset display -> html table change. affected #: 5 files diff -r 0b8c0fda4f852199d12e67cbd7bcdda9a99ac444 -r 5c93ac32ace1b7f61f6c95bba0a0fe04d6f85755 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -255,7 +255,7 @@ else: log.info( "sending stop signal to worker thread" ) self.running = False - if not self.track_jobs_in_database: + if not self.app.config.track_jobs_in_database: self.queue.put( self.STOP_SIGNAL ) self.sleeper.wake() log.info( "job handler queue stopped" ) @@ -352,7 +352,7 @@ else: log.info( "sending stop signal to worker thread" ) self.running = False - if not self.track_jobs_in_database: + if not self.app.config.track_jobs_in_database: self.queue.put( self.STOP_SIGNAL ) self.sleeper.wake() log.info( "job handler stop queue stopped" ) diff -r 0b8c0fda4f852199d12e67cbd7bcdda9a99ac444 -r 5c93ac32ace1b7f61f6c95bba0a0fe04d6f85755 lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -186,7 +186,6 @@ self.queue.put( self.STOP_SIGNAL ) self.sleeper.wake() log.info( "job manager queue stopped" ) - self.dispatcher.shutdown() class JobManagerStopQueue( object ): """ diff -r 0b8c0fda4f852199d12e67cbd7bcdda9a99ac444 -r 5c93ac32ace1b7f61f6c95bba0a0fe04d6f85755 scripts/check_galaxy.py --- a/scripts/check_galaxy.py +++ b/scripts/check_galaxy.py @@ -249,7 +249,7 @@ #return((p.id, p.status)) def diff(self): - self.get("/datasets/%s/display/index" % self.id) + self.get("/datasets/%s/display/display?to_ext=bed" % self.id) data = tc.browser.get_html() tmp = tempfile.mkstemp() dprint("tmp file: %s" % tmp[1]) diff -r 0b8c0fda4f852199d12e67cbd7bcdda9a99ac444 -r 5c93ac32ace1b7f61f6c95bba0a0fe04d6f85755 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -826,13 +826,13 @@ self.assertTrue( genome_build == dbkey ) # Functions associated with user accounts - def create( self, cntrller='user', email='test(a)bx.psu.edu', password='testuser', username='admin-user', webapp='galaxy', referer='' ): + def create( self, cntrller='user', email='test(a)bx.psu.edu', password='testuser', username='admin-user', webapp='galaxy', redirect='' ): # HACK: don't use panels because late_javascripts() messes up the twill browser and it # can't find form fields (and hence user can't be logged in). self.visit_url( "%s/user/create?cntrller=%s&use_panels=False" % ( self.url, cntrller ) ) tc.fv( '1', 'email', email ) tc.fv( '1', 'webapp', webapp ) - tc.fv( '1', 'referer', referer ) + tc.fv( '1', 'redirect', redirect ) tc.fv( '1', 'password', password ) tc.fv( '1', 'confirm', password ) tc.fv( '1', 'username', username ) @@ -936,10 +936,10 @@ self.visit_url( "%s/%s" % ( self.url, url ) ) self.check_page_for_string( 'Default history permissions have been changed.' ) self.home() - def login( self, email='test(a)bx.psu.edu', password='testuser', username='admin-user', webapp='galaxy', referer='' ): + def login( self, email='test(a)bx.psu.edu', password='testuser', username='admin-user', webapp='galaxy', redirect='' ): # test(a)bx.psu.edu is configured as an admin user previously_created, username_taken, invalid_username = \ - self.create( email=email, password=password, username=username, webapp=webapp, referer=referer ) + self.create( email=email, password=password, username=username, webapp=webapp, redirect=redirect ) if previously_created: # The acount has previously been created, so just login. # HACK: don't use panels because late_javascripts() messes up the twill browser and it @@ -947,7 +947,7 @@ self.visit_url( "%s/user/login?use_panels=False" % self.url ) tc.fv( '1', 'email', email ) tc.fv( '1', 'webapp', webapp ) - tc.fv( '1', 'referer', referer ) + tc.fv( '1', 'redirect', redirect ) tc.fv( '1', 'password', password ) tc.submit( 'login_button' ) def logout( self ): @@ -1212,14 +1212,14 @@ # Dataset Security stuff # Tests associated with users def create_new_account_as_admin( self, email='test4(a)bx.psu.edu', password='testuser', - username='regular-user4', webapp='galaxy', referer='' ): + username='regular-user4', webapp='galaxy', redirect='' ): """Create a new account for another user""" # HACK: don't use panels because late_javascripts() messes up the twill browser and it # can't find form fields (and hence user can't be logged in). self.visit_url( "%s/user/create?cntrller=admin" % self.url ) tc.fv( '1', 'email', email ) tc.fv( '1', 'webapp', webapp ) - tc.fv( '1', 'referer', referer ) + tc.fv( '1', 'redirect', redirect ) tc.fv( '1', 'password', password ) tc.fv( '1', 'confirm', password ) tc.fv( '1', 'username', username ) diff -r 0b8c0fda4f852199d12e67cbd7bcdda9a99ac444 -r 5c93ac32ace1b7f61f6c95bba0a0fe04d6f85755 test/functional/test_admin_features.py --- a/test/functional/test_admin_features.py +++ b/test/functional/test_admin_features.py @@ -30,7 +30,7 @@ password=password, username='admin-user', webapp='galaxy', - referer='' ) + redirect='' ) if not username_taken: raise AssertionError, "The public name (%s) is already being used by another user, but no error was displayed" \ % 'admin-user' @@ -40,14 +40,14 @@ password=password, username='h', webapp='galaxy', - referer='' ) + redirect='' ) if not invalid_username: raise AssertionError, "The public name (%s) is is invalid, but no error was displayed" % username previously_created, username_taken, invalid_username = self.create_new_account_as_admin( email=email, password=password, username='regular-user3', webapp='galaxy', - referer='' ) + redirect='' ) # Get the user object for later tests global regular_user3 regular_user3 = get_user( email ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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