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

commit/galaxy-central: carlfeberhard: scatterplot.js: fixes after testing; utils/LazyDataLoader.js: basic lazy ajax loading object;
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d9e8a7eee7aa/ changeset: d9e8a7eee7aa user: carlfeberhard date: 2012-10-11 23:25:51 summary: scatterplot.js: fixes after testing; utils/LazyDataLoader.js: basic lazy ajax loading object; affected #: 3 files diff -r 419d87dd65149285d6c9f0043ea898b365d2dbde -r d9e8a7eee7aac7e0ed15fce27592eb0182144889 static/scripts/utils/LazyDataLoader.js --- /dev/null +++ b/static/scripts/utils/LazyDataLoader.js @@ -0,0 +1,183 @@ +/* +TODO: + ?? superclass dataloader, subclass lazydataloader?? + +*/ +//============================================================================== +/** + * Object to progressively load JSON data from a REST url, delaying some time between loading chunks + * + * Data from ajax loading is aggregated in a list, with one element for each ajax response. + * It's up to the calling code to combine the results in a meaningful, correct way + * + * example: + * var loader = new scatterplot.LazyDataLoader({ + * //logger : console, + * url : ( apiDatasetsURL + '/' + hda.id + '?data_type=raw_data' + * + '&columns=[10,14]' ), + * total : hda.metadata_data_lines, + * size : 500, + * + * initialize : function( config ){ + * // ... do some stuff + * }, + * + * buildUrl : function( start, size ){ + * // change the formation of start, size in query string + * return loader.url + '&' + jQuery.param({ + * start_val: start, + * max_vals: size + * }); + * }, + * + * loadedPartialEvent : 'loader.partial', + * loadedAllEvent : 'loader.all', + * }); + * $( loader ).bind( 'loader.partial', function( event, data ){ + * console.info( 'partial load complete:', event, data ); + * // ... do stuff with new data + * }); + * $( loader ).bind( 'loader.all', function( event, data ){ + * console.info( 'final load complete:', event, data ); + * // ... do stuff with all data + * }); + * + * loader.load( function( dataArray ){ console.debug( 'FINISHED!', x, y, z ); } ); + */ +function LazyDataLoader( config ){ + // for now assume: + // get, async, and params sent via url query string + // we want json + // we know the size of the data on the server beforehand + var loader = this; + + jQuery.extend( loader, LoggableMixin ); + jQuery.extend( loader, { + + //NOTE: the next two need to be sent in config (required) + // total size of data on server + total : undefined, + // url of service to get the data + url : undefined, + + // holds the interval id for the current load delay + currentIntervalId : undefined, + + // optional events to trigger when partial, last data are loaded + // loadedPartialEvent will be sent: the ajax response data, start value, and size + loadedPartialEvent : undefined, + // loadedAllEvent will be sent: the final loader's data array and the total + loadedAllEvent : undefined, + + // each load call will add an element to this array + // it's the responsibility of the code using this to combine them properly + data : [], + // ms btwn recursive loads + delay : 500, + // starting line, element, whatever + start : 0, + // size to fetch per load + size : 1000, + + // loader init func: extends loader with config and calls config.init if there + //@param {object} config : object containing variables to override (or additional) + initialize : function( config ){ + jQuery.extend( loader, config ); + + // call the custom initialize function if any + // only dangerous if the user tries LazyDataLoader.prototype.init + if( config.hasOwnProperty( 'initialize' ) ){ + config.initialize.call( loader, config ); + } + + // ensure necessary stuff + if( !loader.total ){ throw( loader + ' requires a total (total size of the data)' ); } + if( !loader.url ){ throw( loader + ' requires a url' ); } + + this.log( this + ' initialized:', loader ); + }, + + // returns query string formatted start and size (for the next fetch) appended to the loader.url + //OVERRIDE: to change how params are passed, param names, etc. + //@param {int} start : the line/row/datum indicating where in the dataset the next load begins + //@param {int} size : the number of lines/rows/data to get on the next load + buildUrl : function( start, size ){ + // currently VERY SPECIFIC to using data_providers.py start_val, max_vals params + return loader.url + '&' + jQuery.param({ + start_val: start, + max_vals: size + }); + }, + + //OVERRIDE: to handle ajax errors differently + ajaxErrorFn : function( xhr, status, error ){ + alert( loader + ' ERROR:' + status + '\n' + error ); + }, + + // interface to begin load (and first recursive call) + //@param {Function} callback : function to execute when all data is loaded. callback is passed loader.data + load : function( callback ){ + + // subsequent recursive calls + function loadHelper( start, size ){ + loader.log( loader + '.loadHelper, start:', start, 'size:', size ); + var url = loader.buildUrl( start, size ); + loader.log( '\t url:', url ); + + jQuery.ajax({ + url : loader.buildUrl( start, size ), + dataType : 'json', + error : function( xhr, status, error ){ + loader.log( '\t ajax error, status:', status, 'error:', error ); + if( loader.currentIntervalId ){ + clearInterval( loader.currentIntervalId ); + } + loader.ajaxErrorFn( xhr, status, error ); + }, + + success : function( response ){ + var next = start + size, + remainder = Math.min( loader.total - next, loader.size ); + loader.log( '\t ajax success, next:', next, 'remainder:', remainder ); + + // store the response as is in a new element + //TODO:?? store start, size as well? + loader.data.push( response ); + + // fire the partial load event + if( loader.loadedPartialEvent ){ + loader.log( '\t firing:', loader.loadedPartialEvent ); + $( loader ).trigger( loader.loadedPartialEvent, response, start, size ); + } + + // if we haven't gotten everything yet, + // set up for next recursive call and set the timer + if( remainder > 0 ){ + loader.currentIntervalId = setTimeout( + function(){ loadHelper( next, remainder ); }, + loader.delay + ); + loader.log( '\t currentIntervalId:', loader.currentIntervalId ); + + // otherwise (base-case), don't do anything + } else { + loader.log( loader + '.loadHelper, has finished:', loader.data ); + if( loader.loadedAllEvent ){ + loader.log( '\t firing:', loader.loadedAllEvent ); + $( loader ).trigger( loader.loadedAllEvent, loader.data, loader.total ); + } + if( callback ){ callback( loader.data ); } + } + } + }); + } + loadHelper( loader.start, Math.min( loader.total, loader.size ) ); + }, + + toString : function(){ return 'LazyDataLoader'; } + }); + + loader.initialize( config ); + return loader; +} + diff -r 419d87dd65149285d6c9f0043ea898b365d2dbde -r d9e8a7eee7aac7e0ed15fce27592eb0182144889 static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -1,6 +1,8 @@ define([ "../libs/underscore", + "../mvc/base-mvc", + "../utils/LazyDataLoader", "../templates/compiled/template-visualization-scatterplotControlForm", "../templates/compiled/template-visualization-statsTable", "../templates/compiled/template-visualization-chartSettings", @@ -14,7 +16,7 @@ /* ============================================================================= todo: outside this: - BUG: visualization menu doesn't disappear + BUG: setting width, height in plot controls doesn't re-interpolate data locations!! BUG?: get metadata_column_names (from datatype if necessary) BUG: single vis in popupmenu should have tooltip with that name NOT 'Visualizations' @@ -78,7 +80,7 @@ PADDING = 8, X_LABEL_TOO_LONG_AT = 5; - //this.debugging = true; + this.debugging = true; this.log = function(){ if( this.debugging && console && console.debug ){ var args = Array.prototype.slice.call( arguments ); @@ -102,8 +104,8 @@ yNumTicks : 10, xAxisLabelBumpY : 40, yAxisLabelBumpX : -35, - width : 320, - height : 320, + width : 500, + height : 500, //TODO: anyway to make this a sub-obj? marginTop : 50, marginRight : 50, @@ -120,7 +122,7 @@ }; this.config = _.extend( {}, this.defaults, config ); - this.updateConfig = function( newConfig ){ + this.updateConfig = function( newConfig, rerender ){ _.extend( this.config, newConfig ); }; @@ -148,9 +150,10 @@ this.yAxis = this.content.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'y-axis' ); this.yAxisLabel = this.yAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'y-axis-label' ); - this.log( 'built svg:', d3.selectAll( 'svg' ) ); + //this.log( 'built svg:', d3.selectAll( 'svg' ) ); this.adjustChartDimensions = function( top, right, bottom, left ){ + //this.log( this + '.adjustChartDimensions', arguments ); top = top || 0; right = right || 0; bottom = bottom || 0; @@ -171,6 +174,7 @@ // ........................................................ data and scales this.preprocessData = function( data, min, max ){ + //this.log( this + '.preprocessData', arguments ); //TODO: filter by min, max if set // set a cap on the data, limit to first n points @@ -178,7 +182,7 @@ }; this.setUpDomains = function( xCol, yCol, meta ){ - this.log( 'setUpDomains' ); + //this.log( this + '.setUpDomains', arguments ); // configuration takes priority, otherwise meta (from the server) if passed, last-resort: compute it here this.xMin = this.config.xMin || ( meta )?( meta[0].min ):( d3.min( xCol ) ); this.xMax = this.config.xMax || ( meta )?( meta[0].max ):( d3.max( xCol ) ); @@ -187,6 +191,7 @@ }; this.setUpScales = function(){ + //this.log( this + '.setUpScales', arguments ); // Interpolation for x, y based on data domains this.xScale = d3.scale.linear() .domain([ this.xMin, this.xMax ]) @@ -198,6 +203,7 @@ // ........................................................ axis and ticks this.setUpXAxis = function(){ + //this.log( this + '.setUpXAxis', arguments ); // origin: bottom, left //TODO: incoporate top, right this.xAxisFn = d3.svg.axis() @@ -228,13 +234,14 @@ }; this.setUpYAxis = function(){ + //this.log( this + '.setUpYAxis', arguments ); this.yAxisFn = d3.svg.axis() .scale( this.yScale ) .ticks( this.config.yNumTicks ) .orient( 'left' ); this.yAxis// = content.select( 'g#y-axis' ) .call( this.yAxisFn ); - this.log( 'yAxis:', this.yAxis ); + //this.log( 'yAxis:', this.yAxis ); // get the tick labels for the y axis var yTickLabels = this.yAxis.selectAll( 'text' ).filter( function( e, i ){ return i !== 0; } ); @@ -259,7 +266,7 @@ if( this.config.marginLeft < neededY ){ var adjusting = ( neededY ) - this.config.marginLeft; adjusting = ( adjusting < 0 )?( 0 ):( adjusting ); - this.log( 'adjusting:', adjusting ); + //this.log( 'adjusting:', adjusting ); // update dimensions, translations this.adjustChartDimensions( 0, 0, 0, adjusting ); @@ -278,6 +285,7 @@ // ........................................................ grid lines this.renderGrid = function(){ + //this.log( this + '.renderGrid', arguments ); // VERTICAL // select existing this.vGridLines = this.content.selectAll( 'line.v-grid-line' ) @@ -328,51 +336,70 @@ }; + // initial render or complete re-render (REPLACE datapoints) this.renderDatapoints = function( xCol, yCol, ids ){ - // initial render, complete re-render (REPLACE datapoints) + this.log( this + '.renderDatapoints', arguments ); + var count = 0; this.datapoints = this.addDatapoints( xCol, yCol, ids, ".glyph" ); // glyphs that need to be removed: transition to from normal state to 'exit' state, remove from DOM this.datapoints.exit() + .each( function(){ count += 1; } ) .transition().duration( this.config.entryAnimDuration ) .attr( "cy", this.config.height ) .attr( "r", 0 ) .remove(); + this.log( count, ' glyphs removed' ); - this.log( this.datapoints, 'glyphs rendered' ); + //this.log( this.datapoints.length, ' glyphs in the graph' ); }; + // adding points to existing this.addDatapoints = function( newXCol, newYCol, ids, selectorForExisting ){ + this.log( this + '.addDatapoints', arguments ); // ADD datapoints to plot that's already rendered // if selectorForExisting === undefined (as in not passed), addDatapoints won't update existing // pass in the class ( '.glyph' ) to update exising datapoints var plot = this, + count = 0, xPosFn = function( d, i ){ + //if( d ){ this.log( 'x.data:', newXCol[ i ], 'plotted:', plot.xScale( newXCol[ i ] ) ); } return plot.xScale( newXCol[ i ] ); }, yPosFn = function( d, i ){ + //if( d ){ this.log( 'y.data:', newYCol[ i ], 'plotted:', plot.yScale( newYCol[ i ] ) ); } return plot.yScale( newYCol[ i ] ); }; // select all existing glyphs and compare to incoming data // enter() will yield those glyphs that need to be added - var newDatapoints = this.content.selectAll( selectorForExisting ).data( newXCol ); + var newDatapoints = this.content.selectAll( selectorForExisting ); + this.log( 'existing datapoints:', newDatapoints ); + newDatapoints = newDatapoints.data( newXCol ); // enter - new data to be added as glyphs: give them a 'entry' position and style + count = 0; newDatapoints.enter() - .append( "svg:circle" ) + .append( 'svg:circle' ) + .each( function(){ count += 1; } ) .classed( "glyph", true ) - // start all bubbles small... .attr( "cx", xPosFn ) .attr( "cy", yPosFn ) + // start all bubbles small... .attr( "r", 0 ); + this.log( count, ' new glyphs created' ); // for all existing glyphs and those that need to be added: transition anim to final state + count = 0; newDatapoints // ...animate to final position .transition().duration( this.config.entryAnimDuration ) - .attr( "r", this.config.datapointSize ); + .each( function(){ count += 1; } ) + .attr( "cx", xPosFn ) + .attr( "cy", yPosFn ) + .attr( "r", plot.config.datapointSize ); + this.log( count, ' existing glyphs transitioned' ); // attach ids if( ids ){ @@ -419,21 +446,22 @@ }; this.render = function( columnData, meta ){ + this.log( this + '.render', arguments ); //pre: columns passed are numeric //pre: at least two columns are passed //assume: first column is x, second column is y, any remaining aren't used var xCol = columnData[0], yCol = columnData[1], ids = ( columnData.length > 2 )?( columnData[2] ):( undefined ); - this.log( 'renderScatterplot', xCol.length, yCol.length, this.config ); + //this.log( this + '.render', xCol.length, yCol.length, this.config ); //pre: xCol.len == yCol.len xCol = this.preprocessData( xCol ); yCol = this.preprocessData( yCol ); - //this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); + this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); this.setUpDomains( xCol, yCol, meta ); - this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); + //this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); this.setUpScales(); this.adjustChartDimensions(); @@ -515,7 +543,7 @@ this.$chartSettingsPanel = this._render_chartSettings(); this.$statsPanel = this.$el.find( '.tab-pane#chart-stats' ); - this.$el.find( 'ul.nav' ).find( 'a[href="#chart-settings"]' ).tab( 'show' ); + //this.$el.find( 'ul.nav' ).find( 'a[href="#chart-settings"]' ).tab( 'show' ); return this; }, @@ -523,6 +551,7 @@ var chartControl = this, $chartSettingsPanel = this.$el.find( '.tab-pane#chart-settings' ), // limits for controls (by control/chartConfig id) + //TODO: move into TwoVarScatterplot controlRanges = { 'maxDataPoints' : { min: 1000, max: 30000, step: 100 }, 'datapointSize' : { min: 2, max: 10, step: 1 }, @@ -559,7 +588,6 @@ }); //TODO: anim checkbox - //TODO: labels -> renderPlot return $chartSettingsPanel; }, @@ -639,7 +667,7 @@ columns = []; this.log( 'columnSelections:', columnSelections ); - //TODO: ?? could be moved into getColumnVals; + //TODO: move this data/chart settings form crap out this.log( columnSelections.X.val, columnSelections.Y.val ); this.xColIndex = columnSelections.X.colIndex; this.yColIndex = columnSelections.Y.colIndex; @@ -650,15 +678,18 @@ columns.push( columnSelections.ID.colIndex ); } - this.log( columnSelections.X.colName, columnSelections.Y.colName ); - this.plot.xLabel = this.chartConfig.xLabel = columnSelections.X.colName; - this.plot.xLabel = this.chartConfig.yLabel = columnSelections.Y.colName; + // update labels using chartSettings inputs (if not at defaults), otherwise the selects' colName + var chartSettingsXLabel = this.$chartSettingsPanel.find( 'input#X-axis-label' ).val(), + chartSettingsYLabel = this.$chartSettingsPanel.find( 'input#Y-axis-label' ).val(); + this.chartConfig.xLabel = ( chartSettingsXLabel === 'X' )? + ( columnSelections.X.colName ):( chartSettingsXLabel ); + this.chartConfig.yLabel = ( chartSettingsYLabel === 'Y' )? + ( columnSelections.Y.colName ):( chartSettingsYLabel ); + //this.log( 'this.chartConfig:', this.chartConfig ); + view.plot.updateConfig( this.chartConfig, false ); - //TODO: alter directly - view.plot.updateConfig( this.chartConfig, false ); //TODO: validate columns - minimally: we can assume either set by selectors or via a good query string //TODO: other vals: max, start, page - //TODO: chart config // fetch the data, sending chosen columns to the server var params = { @@ -705,6 +736,7 @@ //============================================================================== return { + LazyDataLoader : LazyDataLoader, TwoVarScatterplot : TwoVarScatterplot, ScatterplotControlForm : ScatterplotControlForm };}); diff -r 419d87dd65149285d6c9f0043ea898b365d2dbde -r d9e8a7eee7aac7e0ed15fce27592eb0182144889 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -209,7 +209,7 @@ var hda = ${h.to_json_string( hda )}, historyID = '${historyID}' apiDatasetsURL = "${h.url_for( controller='/api/datasets' )}"; - + var settingsForm = new scatterplot.ScatterplotControlForm({ dataset : hda, el : $( '#chart-settings-form' ), @@ -243,3 +243,4 @@ <div id="test"></div></%def> + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix minor typos in db_shell.py
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/419d87dd6514/ changeset: 419d87dd6514 user: dan date: 2012-10-11 22:43:37 summary: Fix minor typos in db_shell.py affected #: 1 file diff -r 26a72076eb75683e1fe1dca95e1a356f501d9393 -r 419d87dd65149285d6c9f0043ea898b365d2dbde scripts/db_shell.py --- a/scripts/db_shell.py +++ b/scripts/db_shell.py @@ -1,14 +1,14 @@ # This script allows easy access to Galaxy's database layer via the -# Galaxy models. For example:q -# % python -i scripts/db_shel.py +# Galaxy models. For example: +# % python -i scripts/db_shell.py # >>> new_user = User("admin(a)gmail.com") # >>> new_user.set_password # >>> sa_session.add(new_user) # >>> sa_session.commit() # >>> sa_session.query(User).all() # -# You can also use this script as a library, for instance see https://gist.github.com/1979583q -# TODO: This script overlaps alot wth manage_db.py and create_db.py, +# You can also use this script as a library, for instance see https://gist.github.com/1979583 +# TODO: This script overlaps a lot with manage_db.py and create_db.py, # these should maybe be refactored to remove duplication. import sys, os.path, logging 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: 4 new changesets
by Bitbucket 11 Oct '12

11 Oct '12

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d2258c1bcbc9/ changeset: d2258c1bcbc9 user: dan date: 2012-10-11 22:36:45 summary: Unicode fixes for copying datasets. affected #: 1 file diff -r 7549962ac83381ab92ac806b168d45b0b4b9a107 -r d2258c1bcbc9344dc376c11fceeec039b1b23709 templates/dataset/copy_view.mako --- a/templates/dataset/copy_view.mako +++ b/templates/dataset/copy_view.mako @@ -57,7 +57,7 @@ %><option value="${trans.security.encode_id(hist.id)}" ${selected}> - ${i + 1}: ${h.truncate(hist.name, 30)}${current_history_text} + ${i + 1}: ${h.truncate(util.unicodify( hist.name ), 30)}${current_history_text} </option> %endfor </select> @@ -98,7 +98,7 @@ if encoded_id == target_history_id: selected = " selected='selected'" %> - <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate(hist.name, 30)}${source_history_text}</option> + <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate( util.unicodify( hist.name ), 30)}${source_history_text}</option> %endfor </select><br /><br /><a style="margin-left: 10px;" href="javascript:void(0);" id="select-multiple">Choose multiple histories</a> @@ -113,7 +113,7 @@ %><div class="form-row"><input type="checkbox" name="target_history_ids" id="hist_${encoded_id}" value="${encoded_id}"/> - <label for="hist_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${hist.name}${cur_history_text}</label> + <label for="hist_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${ util.unicodify( hist.name ) }${cur_history_text}</label></div> %endfor </div> https://bitbucket.org/galaxy/galaxy-central/changeset/6ef979d7cab5/ changeset: 6ef979d7cab5 user: dan date: 2012-10-11 22:36:45 summary: Unicode fixes for Galaxy Forms. affected #: 1 file diff -r d2258c1bcbc9344dc376c11fceeec039b1b23709 -r 6ef979d7cab519ceef3727a069a55ec7c5a8c21f templates/form.mako --- a/templates/form.mako +++ b/templates/form.mako @@ -53,7 +53,7 @@ %endif <div class="form" style="margin: 1em"> - <div class="form-title">${form.title}</div> + <div class="form-title">${util.unicodify( form.title )}</div><div class="form-body"><% has_file_input = False https://bitbucket.org/galaxy/galaxy-central/changeset/5f67671bafdf/ changeset: 5f67671bafdf user: dan date: 2012-10-11 22:36:45 summary: Unicode fixes for sharing histories. affected #: 1 file diff -r 6ef979d7cab519ceef3727a069a55ec7c5a8c21f -r 5f67671bafdfb3fa4986f1059035bbf177f586f8 templates/history/share.mako --- a/templates/history/share.mako +++ b/templates/history/share.mako @@ -20,7 +20,7 @@ <tr><td><input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - ${history.name} + ${ util.unicodify( history.name )} </td><td> %if len( history.datasets ) < 1: @@ -81,7 +81,7 @@ %for history, hdas in no_change_needed.items(): <div class="form-row"><label>History</label> - ${history.name} + ${util.unicodify( history.name )} </div><div style="clear: both"></div><div class="form-row"> @@ -89,7 +89,7 @@ </div> %for hda in hdas: <div class="form-row"> - ${hda.name} + ${util.unicodify( hda.name )} %if hda.deleted: (deleted) %endif @@ -108,7 +108,7 @@ %for history, hdas in can_change.items(): <div class="form-row"><label>History</label> - ${history.name} + ${util.unicodify( history.name )} </div><div style="clear: both"></div><div class="form-row"> @@ -116,7 +116,7 @@ </div> %for hda in hdas: <div class="form-row"> - ${hda.name} + ${util.unicodify( hda.name )} %if hda.deleted: (deleted) %endif @@ -136,7 +136,7 @@ %for history, hdas in cannot_change.items(): <div class="form-row"><label>History</label> - ${history.name} + ${util.unicodify( history.name )} </div><div style="clear: both"></div><div class="form-row"> @@ -144,7 +144,7 @@ </div> %for hda in hdas: <div class="form-row"> - ${hda.name} + ${util.unicodify( hda.name )} %if hda.deleted: (deleted) %endif https://bitbucket.org/galaxy/galaxy-central/changeset/26a72076eb75/ changeset: 26a72076eb75 user: dan date: 2012-10-11 22:36:46 summary: Unicode fixes for workflow configuration menu. affected #: 1 file diff -r 5f67671bafdfb3fa4986f1059035bbf177f586f8 -r 26a72076eb75683e1fe1dca95e1a356f501d9393 templates/workflow/configure_menu.mako --- a/templates/workflow/configure_menu.mako +++ b/templates/workflow/configure_menu.mako @@ -31,7 +31,7 @@ %for i, workflow in enumerate( workflows ): <tr><td> - ${workflow.name} + ${util.unicodify( workflow.name )} </td><td>You</td><td>${len(workflow.latest_workflow.steps)}</td> @@ -53,7 +53,7 @@ <% workflow = association.stored_workflow %><tr><td> - ${workflow.name} + ${util.unicodify( workflow.name )} </td><td>${workflow.user.email}</td><td>${len(workflow.latest_workflow.steps)}</td> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 11 Oct '12

11 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3fc27b7125cc/ changeset: 3fc27b7125cc user: dan date: 2012-10-11 20:06:10 summary: Only allow errors to be viewed if the user can access the dataset. affected #: 1 file diff -r b27aa5db944d3c3a79c9bedf9d91fe2a2e89e01d -r 3fc27b7125ccca13354558e355832de8f1f5f51a lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -166,6 +166,8 @@ @web.expose def errors( self, trans, id ): hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) + if not hda or not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): + return trans.show_error_message( "Either this dataset does not exist or you do not have permission to access it." ) return trans.fill_template( "dataset/errors.mako", hda=hda ) @web.expose def stdoutX( self, trans, dataset_id=None, **kwargs ): https://bitbucket.org/galaxy/galaxy-central/changeset/7549962ac833/ changeset: 7549962ac833 user: dan date: 2012-10-11 20:06:18 summary: Only copy the user on bug reports if the user can access the dataset. affected #: 1 file diff -r 3fc27b7125ccca13354558e355832de8f1f5f51a -r 7549962ac83381ab92ac806b168d45b0b4b9a107 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -248,7 +248,7 @@ # Check email a bit email = email.strip() parts = email.split() - if len( parts ) == 1 and len( email ) > 0: + if len( parts ) == 1 and len( email ) > 0 and trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): to = to_address + ", " + email else: to = to_address Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 11 Oct '12

11 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/837eb8d9098e/ changeset: 837eb8d9098e user: dan date: 2012-10-11 19:47:10 summary: Fix for viewing errors by bug link on a copied dataset. affected #: 1 file diff -r 046634d0500730333eb181399eaa097b1d9f4343 -r 837eb8d9098ed1e9faa3e651dc7552ef014238fe lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -221,7 +221,7 @@ return trans.show_error_message( "Error reporting has been disabled for this galaxy instance" ) # Get the dataset and associated job hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) - job = hda.creating_job_associations[0].job + job = hda.creating_job # Get the name of the server hosting the Galaxy instance from which this report originated host = trans.request.host history_view_link = "%s/history/view?id=%s" % ( str( host ), trans.security.encode_id( hda.history_id ) ) https://bitbucket.org/galaxy/galaxy-central/changeset/b27aa5db944d/ changeset: b27aa5db944d user: dan date: 2012-10-11 19:47:11 summary: When sending bug report email on a copied dataset, fill in Job info. affected #: 1 file diff -r 837eb8d9098ed1e9faa3e651dc7552ef014238fe -r b27aa5db944d3c3a79c9bedf9d91fe2a2e89e01d templates/dataset/errors.mako --- a/templates/dataset/errors.mako +++ b/templates/dataset/errors.mako @@ -19,9 +19,9 @@ <body><h2>Dataset generation errors</h2><p><b>Dataset ${hda.hid}: ${hda.display_name()}</b></p> - - %if hda.creating_job_associations: - <% job = hda.creating_job_associations[0].job %> + <% job = hda.creating_job %> + %if job: + %if job.traceback: The Galaxy framework encountered the following error while attempting to run the tool: <pre>${ util.unicodify( job.traceback ) | h}</pre> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 11 Oct '12

11 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/32ea61c97ac8/ changeset: 32ea61c97ac8 user: dan date: 2012-10-11 18:28:21 summary: Add creating_job as a property to DatasetInstance. affected #: 1 file diff -r 05dfdda805908059de813a303e6ed02ea5e97117 -r 32ea61c97ac8472a781c9f4056c2044da0d06356 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1261,6 +1261,18 @@ log.warning( e ) return lst return _source_dataset_chain( self, [] ) + @property + def creating_job( self ): + creating_job_associations = None + if self.creating_job_associations: + creating_job_associations = self.creating_job_associations + else: + inherit_chain = self.source_dataset_chain + if inherit_chain: + creating_job_associations = inherit_chain[-1][0].creating_job_associations + if creating_job_associations: + return creating_job_associations[0].job + return None def get_display_applications( self, trans ): return self.datatype.get_display_applications_by_dataset( self, trans ) https://bitbucket.org/galaxy/galaxy-central/changeset/046634d05007/ changeset: 046634d05007 user: dan date: 2012-10-11 18:28:21 summary: Have DatasetInstance controller use .creating_job property for call to _get_job_for_dataset(). affected #: 1 file diff -r 32ea61c97ac8472a781c9f4056c2044da0d06356 -r 046634d0500730333eb181399eaa097b1d9f4343 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -157,14 +157,11 @@ def _get_job_for_dataset( self, trans, dataset_id ): ''' Return the job for the given dataset. This will throw an error if the - dataset is either nonexistent or inaccessible to the user. This looks - up the job by mapping the dataset to an HDA and then mapping the HDA - to its job. This will throw exceptions so that the caller can determine - the appropriate response. + dataset is either nonexistent or inaccessible to the user. ''' hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) assert hda and trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) - return hda.creating_job_associations[0].job + return hda.creating_job @web.expose def errors( self, trans, id ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 11 Oct '12

11 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a21e7bd8a41d/ changeset: a21e7bd8a41d user: dan date: 2012-10-11 18:09:06 summary: Add source_dataset_chain as a property to DatasetInstance. affected #: 1 file diff -r 62b89df24ab159aa12b6a15d63001c4cd01cab2e -r a21e7bd8a41d6d84b9acd63095ea18de80eba76f lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1242,7 +1242,25 @@ return source return ( None, None ) return get_source( self ) - + @property + def source_dataset_chain( self ): + def _source_dataset_chain( dataset, lst ): + try: + cp_from_ldda = dataset.copied_from_library_dataset_dataset_association + if cp_from_ldda: + lst.append( (cp_from_ldda, "(Data Library)") ) + return _source_dataset_chain( cp_from_ldda, lst ) + except Exception, e: + log.warning( e ) + try: + cp_from_hda = dataset.copied_from_history_dataset_association + if cp_from_hda: + lst.append( (cp_from_hda, cp_from_hda.history.name) ) + return _source_dataset_chain( cp_from_hda, lst ) + except Exception, e: + log.warning( e ) + return lst + return _source_dataset_chain( self, [] ) def get_display_applications( self, trans ): return self.datatype.get_display_applications_by_dataset( self, trans ) https://bitbucket.org/galaxy/galaxy-central/changeset/05dfdda80590/ changeset: 05dfdda80590 user: dan date: 2012-10-11 18:09:06 summary: Refactor show_params for hda controller. affected #: 1 file diff -r a21e7bd8a41d6d84b9acd63095ea18de80eba76f -r 05dfdda805908059de813a303e6ed02ea5e97117 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -977,21 +977,6 @@ """ Show the parameters used for an HDA """ - - def source_dataset_chain( dataset, lst ): - try: - cp_from_ldda = dataset.copied_from_library_dataset_dataset_association - cp_from_hda = dataset.copied_from_history_dataset_association - if cp_from_ldda: - lst.append( (cp_from_ldda, "(Data Library)") ) - return source_dataset_chain( cp_from_ldda, lst ) - elif cp_from_hda: - lst.append( (cp_from_hda, cp_from_hda.history.name) ) - return source_dataset_chain( cp_from_hda, lst ) - except: - pass - return lst - hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) if not hda: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) @@ -999,15 +984,17 @@ return trans.show_error_message( "You are not allowed to access this dataset" ) # Get the associated job, if any. If this hda was copied from another, - # we need to find the job that created the origial hda + # we need to find the job that created the origial dataset association. params_objects = None + job = None tool = None - job_hda = hda - while job_hda.copied_from_history_dataset_association: - job_hda = job_hda.copied_from_history_dataset_association - if job_hda.creating_job_associations: - job = None - for assoc in job_hda.creating_job_associations: + inherit_chain = hda.source_dataset_chain + if inherit_chain: + job_dataset_association, dataset_association_container_name = inherit_chain[-1] + else: + job_dataset_association = hda + if job_dataset_association.creating_job_associations: + for assoc in job_dataset_association.creating_job_associations: job = assoc.job break if job: @@ -1020,8 +1007,8 @@ params_objects = job.get_param_values( trans.app ) except: pass - - inherit_chain = source_dataset_chain(hda, []) + if job is None: + return trans.show_error_message( "Job information is not available for this dataset." ) return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, job=job, tool=tool, params_objects=params_objects ) @web.expose Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Do not use backrefs for copied_from_library_dataset/history_dataset_association as it confuses sqlalchemy ('is not available, due to conflicting property').
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/62b89df24ab1/ changeset: 62b89df24ab1 user: dan date: 2012-10-11 17:49:47 summary: Do not use backrefs for copied_from_library_dataset/history_dataset_association as it confuses sqlalchemy ('is not available, due to conflicting property'). affected #: 1 file diff -r 1b031693bd3470172c90533726e4ad6dd7d54e5f -r 62b89df24ab159aa12b6a15d63001c4cd01cab2e lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1222,14 +1222,21 @@ Dataset, primaryjoin=( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ), lazy=False ), # .history defined in History mapper + copied_from_history_dataset_association=relation( + HistoryDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), + remote_side=[HistoryDatasetAssociation.table.c.id], + uselist=False ), copied_to_history_dataset_associations=relation( HistoryDatasetAssociation, - primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), - backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id], uselist=False ) ), + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ) ), + copied_from_library_dataset_dataset_association=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), + uselist=False ), copied_to_library_dataset_dataset_associations=relation( LibraryDatasetDatasetAssociation, - primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), - backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id], uselist=False ) ), + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ), implicitly_converted_datasets=relation( ImplicitlyConvertedDatasetAssociation, primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ), @@ -1484,14 +1491,21 @@ library_dataset = relation( LibraryDataset, primaryjoin=( LibraryDatasetDatasetAssociation.table.c.library_dataset_id == LibraryDataset.table.c.id ) ), user=relation( User.mapper ), + copied_from_library_dataset_dataset_association=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), + remote_side=[LibraryDatasetDatasetAssociation.table.c.id], + uselist=False ), copied_to_library_dataset_dataset_associations=relation( LibraryDatasetDatasetAssociation, - primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), - backref=backref( "copied_from_library_dataset_dataset_association", primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id] ) ), + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ), + copied_from_history_dataset_association=relation( + HistoryDatasetAssociation, + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), + uselist=False ), copied_to_history_dataset_associations=relation( HistoryDatasetAssociation, - primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), - backref=backref( "copied_from_library_dataset_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id], uselist=False ) ), + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ), implicitly_converted_datasets=relation( ImplicitlyConvertedDatasetAssociation, primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id == LibraryDatasetDatasetAssociation.table.c.id ) ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Circster: support data indexing and loading for datasets not previously indexed. Also add visual indicator when drawing/loading tracks.
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1b031693bd34/ changeset: 1b031693bd34 user: jgoecks date: 2012-10-11 16:31:13 summary: Circster: support data indexing and loading for datasets not previously indexed. Also add visual indicator when drawing/loading tracks. affected #: 5 files diff -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 -r 1b031693bd3470172c90533726e4ad6dd7d54e5f lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -184,9 +184,15 @@ chrom = chrom_info[ 'chrom' ] chrom_len = chrom_info[ 'len' ] chrom_data = self.get_data( chrom, 0, chrom_len, **kwargs ) - if chrom_data: - chrom_data[ 'region' ] = "%s:%i-%i" % ( chrom, 0, chrom_len ) - genome_data.append( chrom_data ) + # FIXME: data providers probably should never return None. + # Some data providers return None when there's no data, so + # create a dummy dict if necessary. + if not chrom_data: + chrom_data = { + 'data': None + } + chrom_data[ 'region' ] = "%s:%i-%i" % ( chrom, 0, chrom_len ) + genome_data.append( chrom_data ) return { 'data': genome_data, diff -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 -r 1b031693bd3470172c90533726e4ad6dd7d54e5f lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -52,7 +52,7 @@ elif data_type == 'track_config': rval = self.get_new_track_config( trans, dataset ) elif data_type == 'genome_data': - rval = self._get_genome_data( self, trans, dataset, kwd.get('dbkey', None) ) + rval = self._get_genome_data( trans, dataset, kwd.get('dbkey', None) ) else: # Default: return dataset as API value. rval = dataset.get_api_value() @@ -89,12 +89,13 @@ if msg: return msg - # Check for data in the genome window. - data_provider_registry = trans.app.data_provider_registry - data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset= dataset, source='index' ) - if not data_provider.has_data( chrom ): - return messages.NO_DATA - + # If there is a chrom, check for data on the chrom. + if chrom: + data_provider_registry = trans.app.data_provider_registry + data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset= dataset, source='index' ) + if not data_provider.has_data( chrom ): + return messages.NO_DATA + # Have data if we get here return { "status": messages.DATA, "valid_chroms": None } diff -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 -r 1b031693bd3470172c90533726e4ad6dd7d54e5f static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -143,9 +143,12 @@ initialize: function(options) { this.options = options; this.options.bg_stroke = 'ccc'; + // Fill color when loading data. + this.options.loading_bg_fill = '000'; + // Fill color when data has been loaded. this.options.bg_fill = 'ccc'; this.options.chroms_layout = this._chroms_layout(); - this.options.data_bounds = this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome)); + this.options.data_bounds = []; this.options.scale = 1; this.options.parent_elt = null; }, @@ -154,34 +157,49 @@ * Render track's data by adding SVG elements to parent. */ render: function(parent) { - // Create track group element. + // -- Create track group element. -- this.options.parent_elt = parent.append("g").attr("id", "parent-" + this.options.track_index); var track_parent_elt = this.options.parent_elt; - // Render background arcs. + // -- Render background arcs. -- var genome_arcs = this.options.chroms_layout, arc_gen = d3.svg.arc() .innerRadius(this.options.radius_bounds[0]) .outerRadius(this.options.radius_bounds[1]), + // Attach data to group element. chroms_elts = track_parent_elt.selectAll('g') - .data(genome_arcs).enter().append('svg:g'); + .data(genome_arcs).enter().append('svg:g'), - // Draw arcs. - chroms_elts.append("path") - .attr("d", arc_gen) - .style("stroke", this.options.bg_stroke) - .style("fill", this.options.bg_fill) - .append("title").text(function(d) { return d.data.chrom; }); + // Draw chrom arcs/paths. + chroms_paths = chroms_elts.append("path") + .attr("d", arc_gen) + .style("stroke", this.options.bg_stroke) + .style("fill", this.options.loading_bg_fill); + + // Append titles to paths. + chroms_paths.append("title").text(function(d) { return d.data.chrom; }); - // Render track data. - this._render_data(track_parent_elt); + // -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. -- - // Apply prefs. - var prefs = this.options.track.get('prefs'), - block_color = prefs.block_color; - if (!block_color) { block_color = prefs.color; } - track_parent_elt.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); + var self = this, + data_manager = self.options.track.get('data_manager'), + // If track has a data manager, get deferred that resolves when data is ready. + data_ready_deferred = (data_manager ? data_manager.data_is_ready() : true ); + + // When data is ready, render track. + $.when(data_ready_deferred).then(function() { + $.when(self._render_data(track_parent_elt)).then(function() { + // Apply prefs to all track data. + // TODO: move to _render_data? + var prefs = self.options.track.get('prefs'), + block_color = prefs.block_color; + if (!block_color) { block_color = prefs.color; } + track_parent_elt.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); + + chroms_paths.style("fill", self.options.bg_fill); + }); + }); }, /** @@ -243,7 +261,7 @@ * Update data bounds. */ _update_data_bounds: function() { - this.options.data_bounds = this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome)); + //this.options.data_bounds = this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome)); // TODO: transition all paths to use the new data bounds. }, @@ -255,8 +273,13 @@ var self = this, chrom_arcs = this.options.chroms_layout, track = this.options.track, - genome_wide_data = track.get_genome_wide_data(this.options.genome), - + rendered_deferred = $.Deferred(); + + // When genome-wide data is available, render data. + $.when(track.get('data_manager').get_genome_wide_data(this.options.genome)).then(function(genome_wide_data) { + // Set bounds. + self.options.data_bounds = self.get_data_bounds(genome_wide_data); + // Merge chroms layout with data. layout_and_data = _.zip(chrom_arcs, genome_wide_data), @@ -267,7 +290,10 @@ return self._render_chrom_data(svg, chrom_arc, data); }); - return svg; + rendered_deferred.resolve(svg); + }); + + return rendered_deferred; }, /** @@ -348,7 +374,7 @@ */ _render_chrom_data: function(svg, chrom_arc, chrom_data) { // If no chrom data, return null. - if (!chrom_data || typeof chrom_data === "string" || chrom_data.data.length === 0) { + if (typeof chrom_data === "string" || !chrom_data.data || chrom_data.data.length === 0) { return null; } @@ -407,7 +433,7 @@ get_data_bounds: function(data) { // Get max across data. var max_data = _.map(data, function(d) { - if (!d || typeof d === 'string') { return 0; } + if (typeof d === 'string' || !d.max) { return 0; } return d.max; }); return [ 0, (max_data && typeof max_data !== 'string' ? _.max(max_data) : 0) ]; diff -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 -r 1b031693bd3470172c90533726e4ad6dd7d54e5f static/scripts/viz/sweepster.js --- a/static/scripts/viz/sweepster.js +++ b/static/scripts/viz/sweepster.js @@ -928,7 +928,7 @@ }, output.first().get('track_config')), track_obj = tracks.object_from_template(track_config, self, null); - // Track uses only raw data. + // Track uses raw data. track_obj.data_manager.set('data_type', 'raw_data'); // Set track block colors. diff -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 -r 1b031693bd3470172c90533726e4ad6dd7d54e5f static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -136,6 +136,7 @@ var GenomeDataManager = Cache.extend({ defaults: _.extend({}, Cache.prototype.defaults, { dataset: null, + init_data: null, filters_manager: null, data_type: "data", data_mode_compatible: function(entry, mode) { return true; }, @@ -143,18 +144,52 @@ }), /** + * Initialization. + */ + initialize: function(options) { + Cache.prototype.initialize.call(this); + + // Set initial entries in data manager. + var initial_entries = this.get('init_data'); + if (initial_entries) { + this.add_data(initial_entries); + } + }, + + /** + * Add data entries to manager; each entry should be a dict with attributes region (key), data, and data_type. + * If necessary, manager size is increased to hold all data. + */ + add_data: function(entries) { + // Increase size to accomodate all entries. + if (this.get('num_elements') < entries.length) { + this.set('num_elements', entries.length); + } + + // Put data into manager. + var self = this; + _.each(entries, function(entry) { + self.set_data(entry.region, entry); + }); + }, + + /** * Returns deferred that resolves to true when dataset is ready (or false if dataset * cannot be used). */ data_is_ready: function() { var dataset = this.get('dataset'), ready_deferred = $.Deferred(), + // If requesting raw data, query dataset state; if requesting (converted) data, + // need to query converted datasets state. + query_type = (this.get('data_type') == 'raw_data' ? 'state' : + this.get('data_type') == 'data' ? 'converted_datasets_state' : "error" ), ss_deferred = new util_mod.ServerStateDeferred({ ajax_settings: { url: this.get('dataset').url(), data: { hda_ldda: dataset.get('hda_ldda'), - data_type: 'state' + data_type: query_type }, dataType: "json" }, @@ -312,8 +347,7 @@ // Get additional data, append to current data, and set new data. Use a custom deferred object // to signal when new data is available. // - var - data_manager = this, + var data_manager = this, new_data_request = this.load_data(query_region, mode, resolution, extra_params), new_data_available = $.Deferred(); // load_data sets cache to new_data_request, but use custom deferred object so that signal and data @@ -372,6 +406,49 @@ entry.stale = true; return entry; }, + + /** + * Returns an array of data with each entry representing one chromosome/contig + * of data or, if data is not available, returns a Deferred that resolves to the + * data when it becomes available. + */ + get_genome_wide_data: function(genome) { + // -- Get all data. -- + + var self = this, + all_data_available = true, + + // Map chromosome info into genome data. + gw_data = _.map(genome.get('chroms_info').chrom_info, function(chrom_info) { + var chrom_data = self.get_elt( + new GenomeRegion({ + chrom: chrom_info.chrom, + start: 0, + end: chrom_info.len + }) + ); + + // Set flag if data is not available. + if (!chrom_data) { all_data_available = false; } + + return chrom_data; + }); + + // -- If all data is available, return it. -- + if (all_data_available) { + return gw_data; + } + + // -- All data is not available, so load from server. -- + + var deferred = $.Deferred(); + $.getJSON(this.get('dataset').url(), { data_type: 'genome_data' }, function(genome_wide_data) { + self.add_data(genome_wide_data.data); + deferred.resolve(genome_wide_data.data); + }); + + return deferred; + }, /** * Get data from the cache. @@ -397,7 +474,6 @@ }, load_data: function(region, mode, resolution, extra_params) { - console.log(region, mode, resolution); if (resolution > 1) { // Now that data is pre-fetched before draw, we don't load reference tracks // unless it's at the bottom level. @@ -598,41 +674,17 @@ this.set('id', options.dataset_id); // Set up data manager. - var data_manager = new GenomeDataManager({ - dataset: this - }); - this.set('data_manager', data_manager); - - // If there's preloaded data, add it to data manager. var preloaded_data = this.get('preloaded_data'); if (preloaded_data) { - // Increase size to accomodate all preloaded data. - data_manager.set('num_elements', preloaded_data.data.length); - - // Put data into manager. - _.each(preloaded_data.data, function(entry) { - data_manager.set_data(entry.region, entry); - }); + preloaded_data = preloaded_data.data } - }, - - /** - * Returns an array of data with each entry representing one chromosome/contig - * of data. - */ - get_genome_wide_data: function(genome) { - var data_manager = this.get('data_manager'); - - // Map chromosome data into track data. - return _.map(genome.get('chroms_info').chrom_info, function(chrom_info) { - return data_manager.get_elt( - new GenomeRegion({ - chrom: chrom_info.chrom, - start: 0, - end: chrom_info.len - }) - ); - }); + else { + preloaded_data = []; + } + this.set('data_manager', new GenomeDataManager({ + dataset: this, + init_data: preloaded_data + })); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: scatterplot.js: minor changes; data_providers/basic.py: ensure numeric stats only on numeric columns;
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/60757a1ab164/ changeset: 60757a1ab164 user: carlfeberhard date: 2012-10-11 16:24:43 summary: scatterplot.js: minor changes; data_providers/basic.py: ensure numeric stats only on numeric columns; affected #: 5 files diff -r 3b9db9c4206602859dee02164aa32a925138866e -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 lib/galaxy/visualization/data_providers/basic.py --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -163,16 +163,19 @@ f.close() for index, meta in enumerate( response[ 'meta' ] ): - count = meta[ 'count' ] - meta[ 'mean' ] = float( meta[ 'sum' ] ) / count + column_type = column_types[ index ] - sorted_data = sorted( response[ 'data' ][ index ] ) - # even data count - - middle_index = count / 2 - 1 - if count % 2 == 0: - meta[ 'median' ] = sum( sorted_data[ middle_index : ( middle_index + 1 ) ] ) / 2.0 + if( column_type == 'float' or column_type == 'int' ): + count = meta[ 'count' ] + meta[ 'mean' ] = float( meta[ 'sum' ] ) / count - else: - meta[ 'median' ] = sorted_data[ middle_index ] + sorted_data = sorted( response[ 'data' ][ index ] ) + # even data count - + middle_index = count / 2 - 1 + if count % 2 == 0: + meta[ 'median' ] = sum( sorted_data[ middle_index : ( middle_index + 1 ) ] ) / 2.0 + + else: + meta[ 'median' ] = sorted_data[ middle_index ] return response diff -r 3b9db9c4206602859dee02164aa32a925138866e -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 static/scripts/templates/compiled/template-visualization-chartSettings.js --- a/static/scripts/templates/compiled/template-visualization-chartSettings.js +++ b/static/scripts/templates/compiled/template-visualization-chartSettings.js @@ -13,7 +13,7 @@ foundHelper = helpers.maxDataPoints; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.maxDataPoints; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Change the maximum number of data points displayable on this graph (higher values will\n load significantly slower)\n </p>\n </div>\n\n <div id=\"datapointSize\" class=\"form-input numeric-slider-input\">\n <label for=\"datapointSize\">Size of data point: </label>\n <div class=\"slider-output\">"; + buffer += escapeExpression(stack1) + "</div>\n <div style=\"clear: both;\"></div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Change the maximum number of data points displayable on this graph (higher values will\n load significantly slower)\n </p>\n </div>\n\n <div id=\"datapointSize\" class=\"form-input numeric-slider-input\">\n <label for=\"datapointSize\">Size of data point: </label>\n <div class=\"slider-output\">"; foundHelper = helpers.datapointSize; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.datapointSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } diff -r 3b9db9c4206602859dee02164aa32a925138866e -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 static/scripts/templates/visualization-templates.html --- a/static/scripts/templates/visualization-templates.html +++ b/static/scripts/templates/visualization-templates.html @@ -97,6 +97,7 @@ <div id="maxDataPoints" class="form-input numeric-slider-input"><label for="maxDataPoints">Maximum data points allowed on graph: </label><div class="slider-output">{{maxDataPoints}}</div> + <div style="clear: both;"></div><div class="slider"></div><p class="form-help help-text-small"> Change the maximum number of data points displayable on this graph (higher values will @@ -152,4 +153,4 @@ </div><input id="render-button" type="button" value="Draw" /> -</script> \ No newline at end of file +</script> diff -r 3b9db9c4206602859dee02164aa32a925138866e -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -1,6 +1,4 @@ define([ - //"../libs/jquery/jquery", - "../libs/underscore", "../mvc/base-mvc", "../templates/compiled/template-visualization-scatterplotControlForm", @@ -13,8 +11,6 @@ "../libs/jquery/jquery-ui-1.8.23.custom.min" ], function(){ - - /* ============================================================================= todo: outside this: @@ -54,6 +50,9 @@ how to know what sort of Tabular the data is? smarter about headers validate columns selection (here or server) + + set stats column names by selected columns + move chart into tabbed area... Scatterplot.mako: multiple plots on one page (small multiples) @@ -103,8 +102,8 @@ yNumTicks : 10, xAxisLabelBumpY : 40, yAxisLabelBumpX : -35, - width : 500, - height : 500, + width : 320, + height : 320, //TODO: anyway to make this a sub-obj? marginTop : 50, marginRight : 50, @@ -456,16 +455,10 @@ */ var ScatterplotControlForm = BaseView.extend( LoggableMixin ).extend({ //logger : console, - tagName : 'form', className : 'scatterplot-settings-form', loadingIndicatorImage : 'loading_large_white_bg.gif', - events : { - 'click #render-button' : 'renderPlot', - 'click #include-id-checkbox' : 'toggleThirdColumnSelector' - }, - initialize : function( attributes ){ if( !attributes || !attributes.dataset ){ @@ -571,6 +564,11 @@ return $chartSettingsPanel; }, + events : { + 'click #render-button' : 'renderPlot', + 'click #include-id-checkbox' : 'toggleThirdColumnSelector' + }, + toggleThirdColumnSelector : function(){ this.$el.find( 'select[name="ID"]' ).parent().toggle(); }, @@ -709,4 +707,4 @@ return { TwoVarScatterplot : TwoVarScatterplot, ScatterplotControlForm : ScatterplotControlForm -};}); \ No newline at end of file +};}); diff -r 3b9db9c4206602859dee02164aa32a925138866e -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -20,11 +20,11 @@ .left-column { float: left; - width: 30%; + width: 40%; } .right-column { - margin-left: 32%; + margin-left: 41%; } div.tab-pane { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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