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commit/galaxy-central: jgoecks: Fixes that (a) simplify data providers framework and (b) make it possible to view different trees in the same nexus file.
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8269f76312af/ changeset: 8269f76312af user: jgoecks date: 2012-10-09 05:33:03 summary: Fixes that (a) simplify data providers framework and (b) make it possible to view different trees in the same nexus file. affected #: 7 files diff -r 02fe49c3d251bd30114dcd616336b73b2e8d1ab2 -r 8269f76312af60e356707bc660b6e9903e402106 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -520,7 +520,7 @@ rval.append( payload ) - return { 'data': rval, 'message': message } + return { 'data': rval, 'dataset_type': self.dataset_type, 'message': message } def write_data_to_file( self, regions, filename ): out = open( filename, "w" ) @@ -550,8 +550,6 @@ for large datasets. """ - dataset_type = 'interval_index' - def get_iterator( self, chrom=None, start=None, end=None ): # Read first line in order to match chrom naming format. line = source.readline() @@ -696,8 +694,6 @@ for large datasets. """ - dataset_type = 'tabix' - def get_iterator( self, chrom, start, end ): # Read first line in order to match chrom naming format. line = source.readline() @@ -1278,7 +1274,7 @@ results.append( payload ) - return { 'data': results, 'message': message } + return { 'data': results, 'dataset_type': self.dataset_type, 'message': message } class GtfTabixDataProvider( TabixDataProvider ): """ diff -r 02fe49c3d251bd30114dcd616336b73b2e8d1ab2 -r 8269f76312af60e356707bc660b6e9903e402106 lib/galaxy/visualization/data_providers/phyloviz/__init__.py --- a/lib/galaxy/visualization/data_providers/phyloviz/__init__.py +++ b/lib/galaxy/visualization/data_providers/phyloviz/__init__.py @@ -7,36 +7,37 @@ class PhylovizDataProvider( BaseDataProvider ): + dataset_type = "phylo" + def __init__( self, original_dataset=None ): super( PhylovizDataProvider, self ).__init__( original_dataset=original_dataset ) - def get_data( self ): - """returns [trees], meta - Trees are actually an array of JsonDicts. It's usually one tree, except in the case of Nexus + def get_data( self, tree_index=0 ): + """ + Returns trees. + Trees are actually an array of JsonDicts. It's usually one tree, except in the case of Nexus """ - jsonDicts, meta = [], {} file_ext = self.original_dataset.datatype.file_ext file_name = self.original_dataset.file_name - try: - if file_ext == "nhx": # parses newick files - newickParser = Newick_Parser() - jsonDicts, parseMsg = newickParser.parseFile( file_name ) - elif file_ext == "phyloxml": # parses phyloXML files - phyloxmlParser = Phyloxml_Parser() - jsonDicts, parseMsg = phyloxmlParser.parseFile( file_name ) - elif file_ext == "nex": # parses nexus files - nexusParser = Nexus_Parser() - jsonDicts, parseMsg = nexusParser.parseFile( file_name ) - meta["trees"] = parseMsg - else: - raise Exception("File type is not supported") + parseMsg = None + jsonDicts = [] + rval = { 'dataset_type': self.dataset_type } - meta["msg"] = parseMsg + if file_ext == "nhx": # parses newick files + newickParser = Newick_Parser() + jsonDicts, parseMsg = newickParser.parseFile( file_name ) + elif file_ext == "phyloxml": # parses phyloXML files + phyloxmlParser = Phyloxml_Parser() + jsonDicts, parseMsg = phyloxmlParser.parseFile( file_name ) + elif file_ext == "nex": # parses nexus files + nexusParser = Nexus_Parser() + jsonDicts, parseMsg = nexusParser.parseFile( file_name ) + jsonDicts = jsonDicts[ int( tree_index ) ] + rval["trees"] = parseMsg - except Exception, e: - raise e - jsonDicts, meta["msg"] = [], "Parse failed" + rval[ "data" ] = jsonDicts + rval[ "msg"] = parseMsg + + return rval - return jsonDicts, meta - diff -r 02fe49c3d251bd30114dcd616336b73b2e8d1ab2 -r 8269f76312af60e356707bc660b6e9903e402106 lib/galaxy/visualization/data_providers/registry.py --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -1,5 +1,8 @@ from galaxy.visualization.data_providers.basic import ColumnDataProvider from galaxy.visualization.data_providers.genome import * +from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider +from galaxy.datatypes.xml import Phyloxml +from galaxy.datatypes.data import Newick, Nexus class DataProviderRegistry( object ): """ @@ -45,6 +48,8 @@ data_provider_class = RawVcfDataProvider elif isinstance( original_dataset.datatype, Tabular ): data_provider_class = ColumnDataProvider + elif isinstance( original_dataset.datatype, ( Nexus, Newick, Phyloxml ) ): + data_provider_class = PhylovizDataProvider data_provider = data_provider_class( original_dataset=original_dataset ) diff -r 02fe49c3d251bd30114dcd616336b73b2e8d1ab2 -r 8269f76312af60e356707bc660b6e9903e402106 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -185,19 +185,7 @@ return msg # Return data. - data = None data_provider = trans.app.data_provider_registry.get_data_provider( trans, raw=True, original_dataset=dataset ) - - if isinstance( data_provider, ColumnDataProvider ): - data = data_provider.get_data( **kwargs ) - - else: - # Default to genomic data. - # FIXME: need better way to set dataset_type. - low, high = int( kwargs.get( 'low' ) ), int( kwargs.get( 'high' ) ) - data = data_provider.get_data( start=low, end=high, **kwargs ) - data[ 'dataset_type' ] = 'interval_index' - data[ 'extra_info' ] = None - if isinstance( dataset.datatype, Vcf ): - data[ 'dataset_type' ] = 'tabix' + data = data_provider.get_data( **kwargs ) + return data diff -r 02fe49c3d251bd30114dcd616336b73b2e8d1ab2 -r 8269f76312af60e356707bc660b6e9903e402106 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -847,8 +847,7 @@ # Get data. pd = PhylovizDataProvider( original_dataset=hda ) - json, config = pd.get_data() - json = json[tree_index] + config = pd.get_data( tree_index=tree_index ) config["title"] = hda.display_name() config["ext"] = hda.datatype.file_ext @@ -857,7 +856,7 @@ config["saved_visualization"] = False # Return viz. - return trans.fill_template_mako( "visualization/phyloviz.mako", data = json, config=config ) + return trans.fill_template_mako( "visualization/phyloviz.mako", data = config[ "data" ], config=config ) @web.json def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ): diff -r 02fe49c3d251bd30114dcd616336b73b2e8d1ab2 -r 8269f76312af60e356707bc660b6e9903e402106 static/scripts/viz/phyloviz.js --- a/static/scripts/viz/phyloviz.js +++ b/static/scripts/viz/phyloviz.js @@ -1,4 +1,4 @@ -define(['libs/d3', 'viz/visualization'], function(d3, visualization_mod) { +define(['libs/d3', 'viz/visualization', 'mvc/data'], function(d3, visualization_mod, data_mod) { var UserMenuBase = Backbone.View.extend({ /** @@ -181,6 +181,12 @@ nodeAttrChangedTime : 0 }, + initialize: function(options) { + this.set("dataset", new data_mod.Dataset({ + id: options.dataset_id + })); + }, + root : {}, // Root has to be its own independent object because it is not part of the viz_config toggle : function (d) { @@ -255,7 +261,7 @@ }, success: function(res){ var viz_id = res.url.split("id=")[1].split("&")[0], - viz_url = "/phyloviz/visualization?id=" + viz_id; + viz_url = "/visualization?id=" + viz_id; window.history.pushState({}, "", viz_url + window.location.hash); hide_modal(); } @@ -662,11 +668,11 @@ * Primes the Ajax URL to load another Nexus tree */ var self = this, - treeIndex = $("#phylovizNexSelector :selected").val(), - dataset_id = self.phyloTree.get("dataset_id"), - url = "phyloviz/getJsonData?dataset_id=" + dataset_id + "&treeIndex=" + String(treeIndex); - $.getJSON(url, function(packedJson){ - window.initPhyloViz(packedJson.data, packedJson.config); + treeIndex = $("#phylovizNexSelector :selected").val(); + $.getJSON(self.phyloTree.get("dataset").url(), { tree_index: treeIndex, data_type: 'raw_data' }, function(packedJson){ + self.data = packedJson.data; + self.config = packedJson; + self.render(); }); } }); diff -r 02fe49c3d251bd30114dcd616336b73b2e8d1ab2 -r 8269f76312af60e356707bc660b6e9903e402106 templates/visualization/phyloviz.mako --- a/templates/visualization/phyloviz.mako +++ b/templates/visualization/phyloviz.mako @@ -165,7 +165,7 @@ // -- Render viz. -- phyloviz.render(); - } + }; $(function firstVizLoad(){ // calls when viz is loaded for the first time var config = JSON.parse( '${ h.to_json_string( config )}'); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Add interpreter and absolute path logic to version tag. Thanks to Björn Grüning.
by Bitbucket 08 Oct '12

08 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/02fe49c3d251/ changeset: 02fe49c3d251 user: jgoecks date: 2012-10-08 20:22:44 summary: Add interpreter and absolute path logic to version tag. Thanks to Björn Grüning. affected #: 1 file diff -r 724aaf15bcbe4989450af00c83ea8538c6b2f051 -r 02fe49c3d251bd30114dcd616336b73b2e8d1ab2 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -960,6 +960,12 @@ version_cmd = root.find("version_command") if version_cmd is not None: self.version_string_cmd = version_cmd.text + version_cmd_interpreter = version_cmd.get( "interpreter", None ) + if version_cmd_interpreter: + executable = self.version_string_cmd.split()[0] + abs_executable = os.path.abspath(os.path.join(self.tool_dir, executable)) + command_line = self.version_string_cmd.replace(executable, abs_executable, 1) + self.version_string_cmd = self.interpreter + " " + command_line # Parallelism for tasks, read from tool config. parallelism = root.find("parallelism") if parallelism is not None and parallelism.get("method"): 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: carlfeberhard: history.js: add persistant storage, show prev. opened datasets on page refresh; base-mvc.js: add PersistantStorage object adapter
by Bitbucket 08 Oct '12

08 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/724aaf15bcbe/ changeset: 724aaf15bcbe user: carlfeberhard date: 2012-10-08 19:27:11 summary: history.js: add persistant storage, show prev. opened datasets on page refresh; base-mvc.js: add PersistantStorage object adapter affected #: 3 files diff -r c456d67423b6988de9f9777d9758901845d02de8 -r 724aaf15bcbe4989450af00c83ea8538c6b2f051 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -41,6 +41,7 @@ } }); + //============================================================================== /** * Adds logging capabilities to your Models/Views @@ -69,6 +70,7 @@ } }; + // ============================================================================= /** Global string localization object (and global short form alias) * set with either: @@ -78,8 +80,8 @@ * _l( original ) */ //TODO: move to Galaxy.Localization (maybe galaxy.base.js) -var GalaxyLocalization = jQuery.extend({}, { - aliasName : '_l', +var GalaxyLocalization = jQuery.extend( {}, { + ALIAS_NAME : '_l', localizedStrings : {}, setLocalizedString : function( str_or_obj, localizedString ){ @@ -127,7 +129,7 @@ }); // global localization alias -window[ GalaxyLocalization.aliasName ] = function( str ){ return GalaxyLocalization.localize( str ); }; +window[ GalaxyLocalization.ALIAS_NAME ] = function( str ){ return GalaxyLocalization.localize( str ); }; //TEST: setLocalizedString( string, string ), _l( string ) //TEST: setLocalizedString( hash ), _l( string ) @@ -135,203 +137,112 @@ //TEST: _l( non assigned string ) - //============================================================================== /** - * Base class for template loaders: - * The main interface is loader.getTemplates( templatesToLoad ) - * where templatesToLoad is in the form: - * { - * remoteTemplateFilename1: { - * templateFunctionName1 : templateID1, - * templateFunctionName2 : templateID2, - * ... - * }, - * remoteTemplateFilename2: { - * templateFunctionName3 : templateID3, - * templateFunctionName4 : templateID4, - * ... - * } - * } - * getTemplates will return a map of the templates in the form: - * { - * templateFunctionName1 : compiledTemplateFn1(), - * templateFunctionName2 : compiledTemplateFn2(), - * templateFunctionName3 : compiledTemplateFn3(), - * ... - * } + * @class PersistantStorage + * persistant storage adapter to: + * provide an easy interface to object based storage using method chaining + * allow easy change of the storage engine used (h5's local storage?) * - * Generally meant to be called for Backbone views, etc like this: - * BackboneView.templates = CompiledTemplateLoader( templatesToLoad ); + * @param {String} storageKey : the key the storage engine will place the storage object under + * @param {Object} storageDefaults : [optional] initial object to set up storage with + * + * @example : + * HistoryPanel.storage = new PersistanStorage( HistoryPanel.toString(), { visibleItems, {} }) + * itemView.bind( 'toggleBodyVisibility', function( id, visible ){ + * if( visible ){ + * HistoryPanel.storage.get( 'visibleItems' ).set( id, true ); + * } else { + * HistoryPanel.storage.get( 'visibleItems' ).deleteKey( id ); + * } + * }); */ -var TemplateLoader = _.extend( {}, LoggableMixin, { - //TODO: incorporate caching of template functions (for use across objects) - //TODO: only require and use 2 level (or some variation) map templatesToLoad for the remote loader - - // comment next line out to suppress logging - //logger : console, - - //cachedTemplates : {}, - - getTemplateLoadFn : function(){ - throw( "There is no templateLoadFn. Make sure you're using a subclass of TemplateLoader" ); - }, - - // loop through templatesToLoad assuming it is a map in the form mentioned above - getTemplates : function( templatesToLoad, forceReload ){ - forceReload = forceReload || false; - this.log( this, 'getTemplates:', templatesToLoad, ', forceReload:', forceReload ); - - //!TODO: cache templates here - var templates = {}, - loader = this, - templateLoadFn = this.getTemplateLoadFn(); - - if( !templatesToLoad ){ return templates; } - jQuery.each( templatesToLoad, function( templateFile, templateData ){ - - //TODO: handle flatter map versions of templatesToLoad ({ name : id }) - jQuery.each( templateData, function( templateName, templateID ){ - loader.log( loader + ', templateFile:', templateFile, - 'templateName:', templateName, ', templateID:', templateID ); - templates[ templateName ] = templateLoadFn.call( loader, templateFile, templateName, templateID ); - }); - }); - return templates; +var PersistantStorage = function( storageKey, storageDefaults ){ + if( !storageKey ){ + throw( "PersistantStorage needs storageKey argument" ); } -}); + storageDefaults = storageDefaults || {}; + // ~constants for the current engine + //TODO:?? this would be greatly simplified if we're IE9+ only (setters/getters) + var STORAGE_ENGINE_GETTER = jQuery.jStorage.get, + STORAGE_ENGINE_SETTER = jQuery.jStorage.set, + STORAGE_ENGINE_KEY_DELETER = jQuery.jStorage.deleteKey; -//.............................................................................. -/** find the compiled template in Handlebars.templates by templateName - * and return the entire, requested templates map - */ -var CompiledTemplateLoader = _.extend( {}, TemplateLoader, { - getTemplateLoadFn : function(){ return this.loadCompiledHandlebarsTemplate; }, - - // override if new compiler - loadCompiledHandlebarsTemplate : function( templateFile, templateName, templateID ){ - //pre: compiled templates should have been loaded with the mako helper h.templates - // (although these could be dynamically loaded as well?) - this.log( 'getInDomTemplates, templateFile:', templateFile, - 'templateName:', templateName, ', templateID:', templateID ); - - if( !Handlebars.templates || !Handlebars.templates[ templateID ] ){ - throw( 'Template not found: Handlebars.' + templateID - + '. Check your h.templates() call in the mako file that rendered this page' ); - } - this.log( 'found template function:', templateID ); - // really this is just a lookup - return Handlebars.templates[ templateID ]; - } - - //TEST: Handlebars.full NOT runtime - //TEST: no Handlebars - //TEST: bad id - //TEST: Handlebars.runtime, good id -}); + // recursion helper for method chaining access + var StorageRecursionHelper = function( data, parent ){ + //console.debug( 'new StorageRecursionHelper. data:', data ); + data = data || {}; + parent = parent || null; + return { + // get a value from the storage obj named 'key', + // if it's an object - return a new StorageRecursionHelper wrapped around it + // if it's something simpler - return the value + // if this isn't passed a key - return the data at this level of recursion + get : function( key ){ + //console.debug( this + '.get', key ); + if( key === undefined ){ + return data; + } else if( data.hasOwnProperty( key ) ){ + return ( jQuery.type( data[ key ] ) === 'object' )? + ( new StorageRecursionHelper( data[ key ], this ) ) + :( data[ key ] ); + } + return undefined; + }, + // set a value on the current data - then pass up to top to save current entire object in storage + set : function( key, value ){ + //TODO: add parameterless variation setting the data somehow + // ??: difficult bc of obj by ref, closure + //console.debug( this + '.set', key, value ); + data[ key ] = value; + this.save(); + return this; + }, + // remove a key at this level - then save entire (as 'set' above) + deleteKey : function( key ){ + //console.debug( this + '.deleteKey', key ); + delete data[ key ]; + this.save(); + return this; + }, + // pass up the recursion chain (see below for base case) + save : function(){ + //console.debug( this + '.save', parent ); + return parent.save(); + }, + toString : function(){ + return ( 'StorageRecursionHelper(' + data + ')' ); + } + }; + }; -//.............................................................................. -/** find the NON-compiled template templateID in the DOM, compile it (using Handlebars), - * and return the entire, requested templates map - * (Note: for use with Mako.include and multiple templates) - */ -var InDomTemplateLoader = _.extend( {}, TemplateLoader, { - - // override or change if a new compiler (Underscore, etc.) is being used - compileTemplate : function( templateText ){ - // we'll need the compiler - if( !Handlebars || !Handlebars.compile ){ - throw( 'No Handlebars.compile found. You may only have Handlebars.runtime loaded.' - + 'Include handlebars.full for this to work' ); - } - // copy fn ref to this view under the templateName - this.log( 'compiling template:', templateText ); - return Handlebars.compile( templateText ); - }, - - findTemplateInDom : function( templateFile, templateName, templateID ){ - // assume the last is best - return $( 'script#' + templateID ).last(); - }, - - getTemplateLoadFn : function(){ return this.loadInDomTemplate; }, - - loadInDomTemplate : function( templateFile, templateName, templateID ){ - this.log( 'getInDomTemplate, templateFile:', templateFile, - 'templateName:', templateName, ', templateID:', templateID ); - - // find it in the dom by the id and compile - var template = this.findTemplateInDom( templateFile, templateName, templateID ); - if( !template || !template.length ){ - throw( 'Template not found within the DOM: ' + templateID - + '. Check that this template has been included in the page' ); - } - this.log( 'found template in dom:', template.html() ); - return this.compileTemplate( template.html() ); + //??: more readable to make another class? + var returnedStorage = {}; + // attempt to get starting data from engine... + data = STORAGE_ENGINE_GETTER( storageKey ); + + // ...if that fails, use the defaults (and store them) + if( data === null ){ + //console.debug( 'no previous data. using defaults...' ); + data = jQuery.extend( true, {}, storageDefaults ); + STORAGE_ENGINE_SETTER( storageKey, data ); } - //TEST: no compiler - //TEST: good url, good id, in DOM - //TEST: good url, good id, NOT in DOM -}); + // the object returned by this constructor will be a modified StorageRecursionHelper + returnedStorage = new StorageRecursionHelper( data ); + // the base case for save()'s upward recursion - save everything to storage + returnedStorage.save = function( newData ){ + //console.debug( returnedStorage, '.save:', JSON.stringify( returnedStorage.get() ) ); + STORAGE_ENGINE_SETTER( storageKey, returnedStorage.get() ); + }; + // delete function to remove the base data object from the storageEngine + returnedStorage.destroy = function(){ + //console.debug( returnedStorage, '.destroy:' ); + STORAGE_ENGINE_KEY_DELETER( storageKey ); + }; + returnedStorage.toString = function(){ return 'PersistantStorage(' + data + ')'; }; + + return returnedStorage; +}; -//.............................................................................. -/** HTTP GET the NON-compiled templates, append into the DOM, compile them, - * and return the entire, requested templates map - * (for use with dynamically loaded views) - */ -var RemoteTemplateLoader = _.extend( {}, InDomTemplateLoader, { - templateBaseURL : 'static/scripts/templates/', - - getTemplateLoadFn : function(){ return this.loadViaHttpGet; }, - - loadViaHttpGet : function( templateFile, templateName, templateID ){ - var templateBaseURL = 'static/scripts/templates/'; - this.log( 'loadViaHttpGet, templateFile:', templateFile, - 'templateName:', templateName, ', templateID:', templateID, - 'templateBaseURL:', this.templateBaseURL ); - - //??: possibly not the best pattern here... - // try in-dom first (prevent loading the same templateFile for each of its templates) - var template = null; - try { - template = this.loadInDomTemplate( templateFile, templateName, templateID ); - - // if that didn't work, load the templateFile via GET,... - } catch( exception ){ - this.log( 'getInDomTemplate exception:' + exception ); - // handle no compiler exception - if( !Handlebars.compile ){ throw( exception ); } - //TEST: - - this.log( "Couldn't locate template in DOM: " + templateID ); - var loader = this; - var url = templateBaseURL + templateFile; - //??: async : false may cause problems in the long run - jQuery.ajax( url, { - method : 'GET', - async : false, - success : function( data ){ - loader.log( templateFile + ' loaded via GET. Attempting compile...' ); - //...move the templateFile into the DOM and try that again - $( 'body' ).append( data ); - template = loader.loadInDomTemplate( templateFile, templateName, templateID ); - }, - error : function( data, status, xhr ){ - throw( 'Failed to fetch ' + url + ':' + status ); - } - }); - } - if( !template ){ - throw( "Couldn't load or fetch template: " + templateID ); - } - return template; - } - - //TEST: no compiler - //TEST: good url, good id, already local - //TEST: good url, good id, remote load - //TEST: good url, bad template id - //TEST: bad url, error from ajax -}); diff -r c456d67423b6988de9f9777d9758901845d02de8 -r 724aaf15bcbe4989450af00c83ea8538c6b2f051 static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -6,6 +6,8 @@ Backbone.js implementation of history panel TODO: + currently, adding a dataset (via tool execute, etc.) creates a new dataset and refreshes the page + meta: require.js convert function comments to jsDoc style, complete comments @@ -142,8 +144,9 @@ className : "historyItemContainer", // ................................................................................ SET UP - initialize : function(){ + initialize : function( attributes ){ this.log( this + '.initialize:', this, this.model ); + this.visible = attributes.visible; }, // ................................................................................ RENDER MAIN @@ -209,6 +212,7 @@ return buttonDiv; }, + //TODO: ?? the three title buttons render for err'd datasets: is this normal? _render_displayButton : function(){ // don't show display while uploading if( this.model.get( 'state' ) === HistoryItem.STATES.UPLOAD ){ return null; } @@ -608,6 +612,11 @@ if( this.model.get( 'bodyIsShown' ) === false ){ body.hide(); } + if( this.visible ){ + body.show(); + } else { + body.hide(); + } return body; }, @@ -693,14 +702,15 @@ return false; }, - toggleBodyVisibility : function(){ - this.log( this + '.toggleBodyVisibility' ); - this.$el.find( '.historyItemBody' ).toggle(); + toggleBodyVisibility : function( visible ){ + var $body = this.$el.find( '.historyItemBody' ); + $body.toggle(); + this.trigger( 'toggleBodyVisibility', this.model.get( 'id' ), $body.is( ':visible' ) ); }, // ................................................................................ UTILTIY toString : function(){ - var modelString = ( this.model )?( this.model + '' ):( '' ); + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); return 'HistoryItemView(' + modelString + ')'; } }); @@ -708,21 +718,18 @@ //------------------------------------------------------------------------------ //HistoryItemView.templates = InDomTemplateLoader.getTemplates({ -HistoryItemView.templates = CompiledTemplateLoader.getTemplates({ - 'common-templates.html' : { - warningMsg : 'template-warningmessagesmall' - }, - 'history-templates.html' : { - messages : 'template-history-warning-messages', - titleLink : 'template-history-titleLink', - hdaSummary : 'template-history-hdaSummary', - downloadLinks : 'template-history-downloadLinks', - failedMetadata : 'template-history-failedMetaData', - tagArea : 'template-history-tagArea', - annotationArea : 'template-history-annotationArea', - displayApps : 'template-history-displayApps' - } -}); +HistoryItemView.templates = { + warningMsg : Handlebars.templates[ 'template-warningmessagesmall' ], + + messages : Handlebars.templates[ 'template-history-warning-messages' ], + titleLink : Handlebars.templates[ 'template-history-titleLink' ], + hdaSummary : Handlebars.templates[ 'template-history-hdaSummary' ], + downloadLinks : Handlebars.templates[ 'template-history-downloadLinks' ], + failedMetadata : Handlebars.templates[ 'template-history-failedMetaData' ], + tagArea : Handlebars.templates[ 'template-history-tagArea' ], + annotationArea : Handlebars.templates[ 'template-history-annotationArea' ], + displayApps : Handlebars.templates[ 'template-history-displayApps' ] +}; //============================================================================== var HistoryCollection = Backbone.Collection.extend({ @@ -867,22 +874,51 @@ }); //------------------------------------------------------------------------------ +// view for the HistoryCollection (as per current right hand panel) +//var HistoryView = BaseView.extend( LoggableMixin ).extend( UsesStorageMixin ) .extend({ var HistoryView = BaseView.extend( LoggableMixin ).extend({ - // view for the HistoryCollection (as per current right hand panel) // uncomment this out see log messages //logger : console, // direct attachment to existing element el : 'body.historyPage', - + //TODO: add id? + initialize : function(){ this.log( this + '.initialize:', this ); - this.itemViews = []; - var parent = this; + // data that needs to be persistant over page refreshes + this.storage = new PersistantStorage( + 'HistoryView.' + this.model.get( 'id' ), + { visibleItems : {} } + ); + // set up the individual history items/datasets + this.initializeItems(); + }, + + initializeItems : function(){ + this.itemViews = {}; + var historyPanel = this; this.model.items.each( function( item ){ - var itemView = new HistoryItemView({ model: item }); - parent.itemViews.push( itemView ); + var itemId = item.get( 'id' ), + itemView = new HistoryItemView({ + model: item, visible: + historyPanel.storage.get( 'visibleItems' ).get( itemId ) + }); + historyPanel.setUpItemListeners( itemView ); + historyPanel.itemViews[ itemId ] = itemView; + }); + }, + + setUpItemListeners : function( itemView ){ + var HistoryPanel = this; + // use storage to maintain a list of items whose bodies are visible + itemView.bind( 'toggleBodyVisibility', function( id, visible ){ + if( visible ){ + HistoryPanel.storage.get( 'visibleItems' ).set( id, true ); + } else { + HistoryPanel.storage.get( 'visibleItems' ).deleteKey( id ); + } }); }, @@ -907,8 +943,8 @@ var div = $( '<div/>' ), view = this; //NOTE!: render in reverse (newest on top) via prepend (instead of append) - _.each( this.itemViews, function( itemView ){ - view.log( view + '.render_items:', itemView ); + _.each( this.itemViews, function( itemView, viewId ){ + view.log( view + '.render_items:', viewId, itemView ); div.prepend( itemView.render() ); }); return div; @@ -919,12 +955,9 @@ return 'HistoryView(' + nameString + ')'; } }); -//HistoryItemView.templates = InDomTemplateLoader.getTemplates({ -HistoryView.templates = CompiledTemplateLoader.getTemplates({ - 'history-templates.html' : { - historyPanel : 'template-history-historyPanel' - } -}); +HistoryView.templates = { + historyPanel : Handlebars.templates[ 'template-history-historyPanel' ] +}; diff -r c456d67423b6988de9f9777d9758901845d02de8 -r 724aaf15bcbe4989450af00c83ea8538c6b2f051 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -344,7 +344,9 @@ ${parent.javascripts()} ${h.js( - "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", + "libs/jquery/jstorage", + "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", + "libs/json2", "mvc/base-mvc", "mvc/ui" )} @@ -395,10 +397,10 @@ if( pageData.hdaId ){ self.location = "#" + pageData.hdaId; } - - glx_history = new History( pageData.history ).loadDatasetsAsHistoryItems( pageData.hdas ); - glx_history_view = new HistoryView({ model: glx_history }); + var glx_history = new History( pageData.history ).loadDatasetsAsHistoryItems( pageData.hdas ), + glx_history_view = new HistoryView({ model: glx_history }); glx_history_view.render(); + window.glx_history = glx_history; window.glx_history_view = glx_history_view; return; @@ -452,4 +454,4 @@ ${_('Galaxy History')} </%def> -<body class="historyPage"></body> \ No newline at end of file +<body class="historyPage"></body> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Categories method cleanup in the tool shed admin controller, and add the search feature to the Admin Repository grid in the tool shed.
by Bitbucket 08 Oct '12

08 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c456d67423b6/ changeset: c456d67423b6 user: greg date: 2012-10-08 17:02:16 summary: Categories method cleanup in the tool shed admin controller, and add the search feature to the Admin Repository grid in the tool shed. affected #: 3 files diff -r 04290e2842452d00b9a1e62a1fb54b8acfc0826f -r c456d67423b6988de9f9777d9758901845d02de8 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -18,8 +18,7 @@ log = logging.getLogger( __name__ ) class UserListGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same - # in the galaxy webapp. + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. class UserLoginColumn( grids.TextColumn ): def get_value( self, trans, grid, user ): return user.email @@ -61,7 +60,6 @@ return query return query.filter( and_( model.Tool.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter ) ) - # Grid definition title = "Users" model_class = model.User template='/admin/user/grid.mako' @@ -146,8 +144,6 @@ if role.users: return len( role.users ) return 0 - - # Grid definition title = "Roles" model_class = model.Role template='/admin/dataset_security/role/grid.mako' @@ -231,19 +227,14 @@ if group.members: return len( group.members ) return 0 - - # Grid definition title = "Groups" model_class = model.Group template='/admin/dataset_security/group/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", - #key="name", link=( lambda item: dict( operation="Manage users and roles", id=item.id ) ), - attach_popup=True - #filterable="advanced" - ), + attach_popup=True ), UsersColumn( "Users", attach_popup=False ), RolesColumn( "Roles", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), @@ -301,6 +292,30 @@ ] class AdminRepositoryListGrid( RepositoryListGrid ): + columns = [ RepositoryListGrid.NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + RepositoryListGrid.DescriptionColumn( "Synopsis", + key="description", + attach_popup=False ), + RepositoryListGrid.MetadataRevisionColumn( "Metadata Revisions" ), + RepositoryListGrid.UserColumn( "Owner", + model_class=model.User, + link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), + attach_popup=False, + key="User.username" ), + RepositoryListGrid.EmailAlertsColumn( "Alert", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] + columns.append( grids.MulticolFilterColumn( "Search repository name, description", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) operations = [ operation for operation in RepositoryListGrid.operations ] operations.append( grids.GridOperation( "Delete", allow_multiple=False, @@ -507,41 +522,26 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + name = util.restore_text( params.get( 'name', '' ) ).strip() + description = util.restore_text( params.get( 'description', '' ) ).strip() if params.get( 'create_category_button', False ): - name = util.restore_text( params.name ) - description = util.restore_text( params.description ) - error = False if not name or not description: message = 'Enter a valid name and a description' - error = True - elif trans.sa_session.query( trans.app.model.Category ) \ - .filter( trans.app.model.Category.table.c.name==name ) \ - .first(): + status = 'error' + elif get_category_by_name( trans, name ): message = 'A category with that name already exists' - error = True - if error: - return trans.fill_template( '/webapps/community/category/create_category.mako', - name=name, - description=description, - message=message, - status='error' ) + status = 'error' else: # Create the category category = trans.app.model.Category( name=name, description=description ) trans.sa_session.add( category ) + trans.sa_session.flush() message = "Category '%s' has been created" % category.name - trans.sa_session.flush() + status = 'done' trans.response.send_redirect( web.url_for( controller='admin', action='manage_categories', - message=util.sanitize_text( message ), - status='done' ) ) - trans.response.send_redirect( web.url_for( controller='admin', - action='create_category', - message=util.sanitize_text( message ), - status='error' ) ) - else: - name = '' - description = '' + message=message, + status=status ) ) return trans.fill_template( '/webapps/community/category/create_category.mako', name=name, description=description, @@ -623,8 +623,7 @@ if not new_name: message = 'Enter a valid name' status = 'error' - elif category.name != new_name and \ - trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): + elif category.name != new_name and get_category_by_name( trans, name ): message = 'A category with that name already exists' status = 'error' else: @@ -633,10 +632,11 @@ trans.sa_session.add( category ) trans.sa_session.flush() message = "The information has been saved for category '%s'" % ( category.name ) + status = 'done' return trans.response.send_redirect( web.url_for( controller='admin', action='manage_categories', - message=util.sanitize_text( message ), - status='done' ) ) + message=message, + status=status ) ) return trans.fill_template( '/webapps/community/category/edit_category.mako', category=category, message=message, @@ -649,20 +649,31 @@ # What we've done is rendered the search box for the RepositoryListGrid on the grid.mako # template for the CategoryListGrid. See ~/templates/webapps/community/category/grid.mako. # Since we are searching repositories and not categories, redirect to browse_repositories(). - return self.browse_repositories( trans, **kwd ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_repositories', + **kwd ) ) if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "create": - return self.create_category( trans, **kwd ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='create_category', + **kwd ) ) elif operation == "delete": - return self.mark_category_deleted( trans, **kwd ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='mark_category_deleted', + **kwd ) ) elif operation == "undelete": - return self.undelete_category( trans, **kwd ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='undelete_category', + **kwd ) ) elif operation == "purge": - return self.purge_category( trans, **kwd ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='purge_category', + **kwd ) ) elif operation == "edit": - return self.edit_category( trans, **kwd ) - # Render the list view + return trans.response.send_redirect( web.url_for( controller='admin', + action='edit_category', + **kwd ) ) return self.manage_category_list_grid( trans, **kwd ) @web.expose @web.require_admin diff -r 04290e2842452d00b9a1e62a1fb54b8acfc0826f -r c456d67423b6988de9f9777d9758901845d02de8 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -76,8 +76,6 @@ viewable_repositories += 1 return viewable_repositories return 0 - - # Grid definition title = "Categories of valid repositories" model_class = model.Category template='/webapps/community/category/valid_grid.mako' @@ -146,15 +144,6 @@ if column_filter == "All": return query return query.filter( model.Category.name == column_filter ) - class DeletedColumn( grids.DeletedColumn ): - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "Active" : "False", "Deactivated or uninstalled" : "True", "All": "All" } - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): if repository.user: @@ -179,8 +168,7 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), DescriptionColumn( "Synopsis", key="description", @@ -207,10 +195,10 @@ model_class=model.Category, key="Category.name", visible=False ), - DeletedColumn( "Status", - key="deleted", - visible=False, - filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, description", cols_to_filter=[ columns[0], columns[1] ], diff -r 04290e2842452d00b9a1e62a1fb54b8acfc0826f -r c456d67423b6988de9f9777d9758901845d02de8 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -55,6 +55,15 @@ class ToolShedColumn( grids.TextColumn ): def get_value( self, trans, grid, tool_shed_repository ): return tool_shed_repository.tool_shed + class DeletedColumn( grids.DeletedColumn ): + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = { "Active" : "False", "Deactivated or uninstalled" : "True", "All": "All" } + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters # Grid definition title = "Installed tool shed repositories" model_class = model.ToolShedRepository @@ -74,10 +83,10 @@ filterable="advanced" ), ToolShedColumn( "Tool shed" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) + DeletedColumn( "Status", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search repository name", cols_to_filter=[ columns[0] ], Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Make the DeletedColumn in the Repositories grid a subclass so that the Advanced search labels clarify the status of the filtered repositories.
by Bitbucket 08 Oct '12

08 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/04290e284245/ changeset: 04290e284245 user: greg date: 2012-10-08 16:30:43 summary: Make the DeletedColumn in the Repositories grid a subclass so that the Advanced search labels clarify the status of the filtered repositories. affected #: 1 file diff -r 685a17af92dfd6a2e3d7e3c9a3a4b119c78a6f96 -r 04290e2842452d00b9a1e62a1fb54b8acfc0826f lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -40,8 +40,6 @@ viewable_repositories += 1 return viewable_repositories return 0 - - # Grid definition title = "Categories" model_class = model.Category template='/webapps/community/category/grid.mako' @@ -148,6 +146,15 @@ if column_filter == "All": return query return query.filter( model.Category.name == column_filter ) + class DeletedColumn( grids.DeletedColumn ): + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = { "Active" : "False", "Deactivated or uninstalled" : "True", "All": "All" } + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): if repository.user: @@ -200,10 +207,10 @@ model_class=model.Category, key="Category.name", visible=False ), - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) + DeletedColumn( "Status", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, description", cols_to_filter=[ columns[0], columns[1] ], @@ -2182,7 +2189,10 @@ cntrller = params.get( 'cntrller', 'repository' ) repository = get_repository( trans, id ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) - metadata = repository_metadata.metadata + if repository_metadata: + metadata = repository_metadata.metadata + else: + metadata = None if metadata and 'readme' in metadata: readme_file = str( metadata[ 'readme' ] ) repo_files_dir = repository.repo_path 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: Add logical operators to the compute tool whitelist.
by Bitbucket 08 Oct '12

08 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/685a17af92df/ changeset: 685a17af92df user: natefoo date: 2012-10-08 16:28:29 summary: Add logical operators to the compute tool whitelist. affected #: 1 file diff -r 26dfa56403e1011445854560b3e9818180b3c8c2 -r 685a17af92dfd6a2e3d7e3c9a3a4b119c78a6f96 tools/stats/column_maker.py --- a/tools/stats/column_maker.py +++ b/tools/stats/column_maker.py @@ -46,9 +46,10 @@ for key, value in mapped_str.items(): expr = expr.replace( key, value ) +operators = 'is|not|or|and' builtin_and_math_functions = 'abs|all|any|bin|chr|cmp|complex|divmod|float|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|exp|sqrt|ceil|floor' string_and_list_methods = [ name for name in dir('') + dir([]) if not name.startswith('_') ] -whitelist = "^([c0-9\+\-\*\/\.\'\"><=,: ]|%s|%s)*$" % (builtin_and_math_functions, '|'.join(string_and_list_methods)) +whitelist = "^([c0-9\+\-\*\/\.\'\"><=,:! ]|%s|%s|%s)*$" % (operators, builtin_and_math_functions, '|'.join(string_and_list_methods)) if not re.compile(whitelist).match(expr): stop_err("Invalid expression") 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: Another fix needed due to the elimination of the get_webapp() method in the old base controller.
by Bitbucket 08 Oct '12

08 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/26dfa56403e1/ changeset: 26dfa56403e1 user: greg date: 2012-10-08 15:13:18 summary: Another fix needed due to the elimination of the get_webapp() method in the old base controller. affected #: 1 file diff -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 -r 26dfa56403e1011445854560b3e9818180b3c8c2 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -711,7 +711,7 @@ tool_dependencies_dict = {} repository_name = elem.get( 'name' ) changeset_revision = elem.get( 'changeset_revision' ) - url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s&webapp=install_manager' % \ + url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s&from_install_manager=True' % \ ( tool_shed_url, repository_name, changeset_revision ) response = urllib2.urlopen( url ) text = response.read() 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: Enable circster to accept a dataset to add to visualization. Also, make visualization creation more flexible and some small refactoring for JS visualization objects.
by Bitbucket 05 Oct '12

05 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/05fc04a70a3b/ changeset: 05fc04a70a3b user: jgoecks date: 2012-10-05 22:01:55 summary: Enable circster to accept a dataset to add to visualization. Also, make visualization creation more flexible and some small refactoring for JS visualization objects. affected #: 6 files diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -335,16 +335,18 @@ viz_types = [ "trackster", "circster" ] - def create_visualization( self, trans, title, slug, type, dbkey, annotation=None, config={} ): + def create_visualization( self, trans, type, title="Untitled Genome Vis", slug=None, dbkey=None, annotation=None, config={}, save=True ): """ Create visualiation and first revision. """ - visualization = self._create_visualization( trans, title, type, dbkey, slug, annotation ) + visualization = self._create_visualization( trans, title, type, dbkey, slug, annotation, save ) # Create and save first visualization revision revision = trans.model.VisualizationRevision( visualization=visualization, title=title, config=config, dbkey=dbkey ) visualization.latest_revision = revision - session = trans.sa_session - session.add( revision ) - session.flush() + + if save: + session = trans.sa_session + session.add( revision ) + session.flush() return visualization @@ -440,7 +442,7 @@ """ Returns a visualization's configuration. Only works for trackster visualizations right now. """ config = None - if visualization.type == 'trackster': + if visualization.type in [ 'trackster', 'genome' ]: # Unpack Trackster config. latest_revision = visualization.latest_revision bookmarks = latest_revision.config.get( 'bookmarks', [] ) @@ -566,7 +568,7 @@ # -- Helper functions -- - def _create_visualization( self, trans, title, type, dbkey, slug=None, annotation=None ): + def _create_visualization( self, trans, title, type, dbkey=None, slug=None, annotation=None, save=True ): """ Create visualization but not first revision. Returns Visualization object. """ user = trans.get_user() @@ -593,9 +595,10 @@ annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans.sa_session, trans.user, visualization, annotation ) - session = trans.sa_session - session.add( visualization ) - session.flush() + if save: + session = trans.sa_session + session.add( visualization ) + session.flush() return visualization diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -741,20 +741,36 @@ return self.save_visualization( trans, config, type, id, title, dbkey, annotation ) @web.expose - def circster( self, trans, id, **kwargs ): + def circster( self, trans, id=None, hda_ldda=None, dataset_id=None, dbkey=None ): """ Display a circster visualization. """ - vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) + + # Get/create vis. + if id: + # Display existing viz. + vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) + else: + # Create new viz. + vis = self.create_visualization( trans, type="genome", dbkey=dbkey, save=False ) + + # Get the vis config and work with it from here on out. Working with the + # config is only possible because the config structure of trackster/genome + # visualizations is well known. viz_config = self.get_visualization_config( trans, vis ) + # Add dataset if specified. + if dataset_id: + dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) + viz_config[ 'tracks' ].append( self.get_new_track_config( trans, dataset ) ) + # Get genome info. dbkey = viz_config[ 'dbkey' ] chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey ) genome = { 'dbkey': dbkey, 'chroms_info': chroms_info } # Add genome-wide summary tree data to each track in viz. - tracks = viz_config[ 'tracks' ] + tracks = viz_config.get( 'tracks', [] ) for track in tracks: # Get dataset and indexed datatype. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -351,7 +351,6 @@ if (!extra_params) { extra_params = {}; } // Use additional parameters to get more detailed data. - var mode; if (cur_data.dataset_type === 'bigwig') { extra_params.num_samples = cur_data.data.length * detail_multiplier; } @@ -642,21 +641,10 @@ */ var Visualization = Backbone.RelationalModel.extend({ defaults: { - id: '', title: '', - type: '', - dbkey: '', - tracks: null + type: '' }, - relations: [ - { - type: Backbone.HasMany, - key: 'tracks', - relatedModel: BackboneTrack - } - ], - // Use function because visualization_url changes depending on viz. // FIXME: all visualizations should save to the same URL (and hence // this function won't be needed). @@ -682,13 +670,27 @@ }); /** - * A Genome space visualization. + * A visualization of genome data. */ var GenomeVisualization = Visualization.extend({ defaults: _.extend({}, Visualization.prototype.defaults, { + dbkey: '', + tracks: null, bookmarks: null, viewport: null - }) + }), + + relations: [ + { + type: Backbone.HasMany, + key: 'tracks', + relatedModel: BackboneTrack + } + ], + + add_track: function(track) { + this.get('tracks').push(track); + } }); /** @@ -727,6 +729,7 @@ }); return { + BackboneTrack: BackboneTrack, BrowserBookmark: BrowserBookmark, BrowserBookmarkCollection: BrowserBookmarkCollection, Cache: Cache, diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -236,7 +236,10 @@ } return action; }, - params = {dataset_id: dataset_id}; + params = { + dataset_id: dataset_id, + hda_ldda: 'hda' + }; // Add dbkey to params if it exists. if (dbkey) { params['dbkey'] = dbkey; } diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -226,11 +226,7 @@ ## Visualization icon + visualizations. Using anchor attributes is a HACK to encode needed ## information--URL base, dataset id, dbkey, visualizations--in anchor. <% - visualizations = data.get_visualizations() - ## HACK: if there are visualizations, only provide a subset for now - ## since others are not ready. - comment out to see all WIP visualizations - if visualizations: - visualizations = [ vis for vis in visualizations if vis in [ 'trackster', 'phyloviz', 'scatterplot' ] ] + visualizations = data.get_visualizations() %> %if visualizations: <a href="${h.url_for( controller='visualization' )}" diff -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -33,7 +33,7 @@ } }); - require( [ "libs/d3", "viz/visualization", "viz/circster" ], function( d3, visualization, circster ) { + require( [ "viz/visualization", "viz/circster" ], function(visualization, circster ) { $(function() { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 05 Oct '12

05 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b5bda7a5c345/ changeset: b5bda7a5c345 user: natefoo date: 2012-10-05 21:49:26 summary: Fix the Compute tool to only allow for execution of a limited set of expressions. affected #: 1 file diff -r e8fc8e57dadc8a1254d994e4e05f40271d7e856b -r b5bda7a5c34535ada63722941f2a2d62524b1faa tools/stats/column_maker.py --- a/tools/stats/column_maker.py +++ b/tools/stats/column_maker.py @@ -46,6 +46,12 @@ for key, value in mapped_str.items(): expr = expr.replace( key, value ) +builtin_and_math_functions = 'abs|all|any|bin|chr|cmp|complex|divmod|float|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|exp|sqrt|ceil|floor' +string_and_list_methods = [ name for name in dir('') + dir([]) if not name.startswith('_') ] +whitelist = "^([c0-9\+\-\*\/\.\'\"><=,: ]|%s|%s)*$" % (builtin_and_math_functions, '|'.join(string_and_list_methods)) +if not re.compile(whitelist).match(expr): + stop_err("Invalid expression") + # Prepare the column variable names and wrappers for column data types cols, type_casts = [], [] for col in range( 1, in_columns + 1 ): https://bitbucket.org/galaxy/galaxy-central/changeset/3b63335f5b1b/ changeset: 3b63335f5b1b user: natefoo date: 2012-10-05 21:52:50 summary: Merge from galaxy-dist affected #: 1 file diff -r cf93e8aa50f96e4d43d39e817d9754dc41a5886e -r 3b63335f5b1b33a2d6f74c2dfd38b85d97e9eebd tools/stats/column_maker.py --- a/tools/stats/column_maker.py +++ b/tools/stats/column_maker.py @@ -46,6 +46,12 @@ for key, value in mapped_str.items(): expr = expr.replace( key, value ) +builtin_and_math_functions = 'abs|all|any|bin|chr|cmp|complex|divmod|float|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|exp|sqrt|ceil|floor' +string_and_list_methods = [ name for name in dir('') + dir([]) if not name.startswith('_') ] +whitelist = "^([c0-9\+\-\*\/\.\'\"><=,: ]|%s|%s)*$" % (builtin_and_math_functions, '|'.join(string_and_list_methods)) +if not re.compile(whitelist).match(expr): + stop_err("Invalid expression") + # Prepare the column variable names and wrappers for column data types cols, type_casts = [], [] for col in range( 1, in_columns + 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: jgoecks: When finding applicable visualizations, check to ensure that there are column_types before trying to iterate over them.
by Bitbucket 05 Oct '12

05 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cf93e8aa50f9/ changeset: cf93e8aa50f9 user: jgoecks date: 2012-10-05 15:43:04 summary: When finding applicable visualizations, check to ensure that there are column_types before trying to iterate over them. affected #: 1 file diff -r 210c39f4bf7f2d91c68df84dd9ccecb2ff9f93aa -r cf93e8aa50f96e4d43d39e817d9754dc41a5886e lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -309,9 +309,10 @@ # Can visualize tabular data as scatterplot if there are 2+ numerical # columns. num_numerical_cols = 0 - for col_type in dataset.metadata.column_types: - if col_type in [ 'int', 'float' ]: - num_numerical_cols += 1 + if dataset.metadata.column_types: + for col_type in dataset.metadata.column_types: + if col_type in [ 'int', 'float' ]: + num_numerical_cols += 1 vizs = super( Tabular, self ).get_visualizations( dataset ) if num_numerical_cols >= 2: 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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