Created
December 3, 2015 15:37
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Galaxy tool popularity WIP
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| <% | |
| root = h.url_for( "/" ) | |
| app_root = root + "plugins/visualizations/popularity/static/" | |
| title = "Tool popularity derived from dataset '" + hda.name + "'" | |
| ## creating_job = hda.creating_job.id | |
| creating_job = trans.security.encode_id( hda.creating_job.id ) | |
| creating_job_id = hda.creating_job.id | |
| tool1 = hda.creating_job.tool_id | |
| # optionally bootstrap data from dprov | |
| ##data = list( hda.datatype.dataset_column_dataprovider( hda, limit=10000 ) ) | |
| # Use root for resource loading. | |
| root = h.url_for( '/' ) | |
| %> | |
| ## ---------------------------------------------------------------------------- | |
| <!DOCTYPE HTML> | |
| <html> | |
| <head> | |
| <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | |
| <title>${title}</title> | |
| ## ---------------------------------------------------------------------------- | |
| ${h.css( 'base' )} | |
| ## ${h.stylesheet_link( root + 'plugins/visualizations/scatterplot/static/scatterplot.css' )} | |
| ## ---------------------------------------------------------------------------- | |
| ${h.js( 'libs/jquery/jquery', | |
| ## 'libs/jquery/jquery.migrate', | |
| ## 'libs/jquery/jquery-ui', | |
| ## 'libs/bootstrap', | |
| 'libs/require', | |
| 'libs/underscore', | |
| 'libs/backbone/backbone' )} | |
| ## 'libs/d3', | |
| ## 'libs/handlebars.runtime', | |
| ## 'ui/peek-column-selector', | |
| ## 'ui/pagination', | |
| ## 'mvc/visualization/visualization-model' )} | |
| ${h.javascript_link( app_root + 'app.js' )} | |
| <script type="text/javascript"> | |
| /** | |
| * Get a list of popular tools that based on the inputs to the selected dataset. | |
| */ | |
| function getToolList(){ | |
| job1Info = jQuery.ajax( '/api/jobs/${creating_job}' ); | |
| toolIds = [ '${tool1}' ] | |
| job1Info.done( function( response ) { | |
| inputs = response.inputs; | |
| // Look for ID(s) of job(s) preceeding this dataset's job | |
| jobsInfo = [] | |
| jQuery.each(inputs, function( k, v ) { | |
| jobsInfo.push( | |
| jQuery.ajax( '/api/jobs/' + v.id ) | |
| .done( function( jobn ) { | |
| window.console.log(jobn.tool_id); | |
| toolIds.push( jobn.tool_id ); | |
| })); | |
| }); | |
| // A list of tool IDs that are ignorred | |
| ignoreTools = [ 'upload1', '__SET_METADATA__' ]; | |
| // Wait for all the requests to return and filter tool IDs | |
| jQuery.when.apply($, jobsInfo) | |
| .done(function() { | |
| for( i=0; i<ignoreTools.length; i++ ) { | |
| if ( toolIds.indexOf( ignoreTools[i] ) > -1 ) { | |
| // window.console.log("Removing tool on the ignore list: " + ignoreTools[i]); | |
| toolIds.splice( toolIds.indexOf( ignoreTools[i] ), 1 ); | |
| } | |
| } | |
| key = toolIds.join( [ ',' ] ); | |
| window.console.log("key: " + key); | |
| // Given the chain key, get the popular tools | |
| popular = jQuery.ajax( '/api/tools/popular?tool_chain=' + key ); | |
| popular.done( function( response ) { | |
| // window.console.log( response ); | |
| showTools(response); | |
| }); | |
| }); | |
| }); | |
| } | |
| /** | |
| * Parse the tools list and display it. | |
| */ | |
| function showTools(toolsInfo) { | |
| window.console.log(toolsInfo); | |
| tp = toolsInfo.popular; | |
| tools = "<table><tr><th>Tool ID</th><th>Relevance</th></tr>"; | |
| for ( i=0; i<tp.length; i++ ) { | |
| tools += "<tr><td>" + tp[i].tool_id + "</td><td>" + (tp[i].relevance*100).toFixed(2) + "%</td</tr>"; | |
| } | |
| tools += "</table"; | |
| $('#tools-container').html( tools ); | |
| } | |
| </script> | |
| </head> | |
| ## ---------------------------------------------------------------------------- | |
| <body> | |
| <div class="chart-header"> | |
| <h2>${title}</h2> | |
| </div> | |
| <div id="tools-container"> | |
| Please wait - computing tool popularity... | |
| </div> | |
| <script type="text/javascript"> | |
| getToolList(); | |
| // get configuration | |
| // var config = { | |
| // root : '${root}', | |
| // app_root : '${app_root}' | |
| // }; | |
| // // link galaxy | |
| // var Galaxy = Galaxy || parent.Galaxy; | |
| // // console protection | |
| // window.console = window.console || { | |
| // log : function(){}, | |
| // debug : function(){}, | |
| // info : function(){}, | |
| // warn : function(){}, | |
| // error : function(){}, | |
| // assert : function(){} | |
| // }; | |
| // // configure require | |
| // require.config({ | |
| // baseUrl: config.root + "static/scripts/", | |
| // paths: { | |
| // "plugin" : "${app_root}", | |
| // // "d3" : "libs/d3" | |
| // }, | |
| // shim: { | |
| // "libs/underscore": { exports: "_" }, | |
| // "libs/backbone/backbone": { exports: "Backbone" } | |
| // // "d3": { exports: "d3"} | |
| // } | |
| // }); | |
| // // application | |
| // var app = null; | |
| // $(function() { | |
| // // request application script | |
| // require(['plugin/app'], function(App) { | |
| // // load options | |
| // var options = { | |
| // id : ${h.dumps( visualization_id )} || undefined, | |
| // config : ${h.dumps( config )} | |
| // } | |
| // // create application | |
| // app = new App(options); | |
| // // add to body | |
| // $('body').append(app.$el); | |
| // }); | |
| // }); | |
| // get configuration | |
| // var config = { | |
| // root : '${root}', | |
| // app_root : '${app_root}' | |
| // }; | |
| // // configure require | |
| // require.config({ | |
| // baseUrl: config.root + "static/scripts/", | |
| // // paths: { | |
| // // "plugin" : "${app_root}" | |
| // // }, | |
| // // shim: { | |
| // // "libs/underscore": { exports: "_" }, | |
| // // "libs/backbone/backbone": { exports: "Backbone" } | |
| // // } | |
| // }); | |
| // // var app = new PopularityVis(); | |
| // // // application | |
| // var app = null; | |
| // $(function() { | |
| // // request application script | |
| // require(['libs/backbone/backbone'], function( POPULARITY ) { | |
| // $(function(){ | |
| // // create application | |
| // app = new POPULARITY.PopularityVis(); | |
| // // add to body | |
| // $('body').append(app.$el); | |
| // }); | |
| // }); | |
| // }); | |
| // $('#tools-container').text( popular.responseText ); | |
| // window.console.log('title: ' + model.get( 'creating_job' )); | |
| // $(function(){ | |
| // var model = getModel(), | |
| // hdaJSON = getHDAJSON(), | |
| // editor = new ScatterplotConfigEditor({ | |
| // el : $( '.scatterplot-editor' ).attr( 'id', 'scatterplot-editor-hda-' + hdaJSON.id ), | |
| // model : getModel(), | |
| // dataset : hdaJSON | |
| // }).render(); | |
| // window.editor = editor; | |
| // $( '.chart-header h2' ).click( function(){ | |
| // var returned = prompt( 'Enter a new title:' ); | |
| // if( returned ){ | |
| // model.set( 'title', returned ); | |
| // } | |
| // }); | |
| // model.on( 'change:title', function(){ | |
| // $( '.chart-header h2' ).text( model.get( 'title' ) ); | |
| // document.title = model.get( 'title' ) + ' | ' + '${visualization_display_name}'; | |
| // }) | |
| // }); | |
| </script> | |
| </body> |
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| @web.expose_api_anonymous | |
| def popular( self, trans, **kwd ): | |
| """ | |
| * GET /api/tools/popular | |
| Return information about popular tools to use based on provided tools. | |
| The popularity is based on sequences of supplied tools | |
| as used on Galaxy Main from years 2006 to 2015. | |
| :type tool_chain: str | |
| :param tool_chain: a comma-separated list of tool ID's | |
| # Not (yet) implemented | |
| :type filter: list | |
| :param filter: a list of strings by which to filter the results | |
| :rtype: dict | |
| :returns: two keys are included in the returned dict: | |
| - ``tool_chain``: a string of supplied tool ID's; | |
| - ``popular``: a list of dictionaries containing | |
| popular tools. Each dict further contains keys | |
| ``tool_id`` (str), ``relevance`` (str). | |
| """ | |
| rval = {} | |
| chains = {} # Global historic chains (TODO: supply this) | |
| chains = {'join1,Remove beginning1': [{'tool_id': 'T1', 'relevance': '0.43'}, | |
| {'tool_id': 'T2', 'relevance': '0.57'}]} | |
| fp = 'tool-data/total_triplets.json' | |
| with open( fp, 'r') as f: | |
| chains = load(f) | |
| popular = [] # A list of popular tools to return | |
| tool_chain = kwd.get( 'tool_chain', '' ) | |
| if tool_chain: | |
| chain = chains.get( tool_chain, {} ) | |
| for tool_id, relevance in chain.iteritems(): | |
| popular.append( { 'tool_id': tool_id, | |
| 'relevance': relevance } ) | |
| rval[ 'tool_chain' ] = tool_chain | |
| rval[ 'popular' ] = popular | |
| return rval |
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