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

commit/galaxy-central: carlfeberhard: scatterplot: add require.js
by Bitbucket 24 Sep '12

24 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/327632b4f999/ changeset: 327632b4f999 user: carlfeberhard date: 2012-09-24 19:47:23 summary: scatterplot: add require.js affected #: 3 files diff -r 8b7dfceabe3ea6cc15001f05a623157e95f1bcb7 -r 327632b4f9992b2c3f4b9c6f705bed1f4e05914d static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -1,3 +1,9 @@ +define([ + "../libs/underscore", + "../libs/d3", + "../mvc/base-mvc" + +], function(){ /* ============================================================================= todo: outside this: @@ -355,11 +361,11 @@ }; } -//// ugh...this seems like the wrong way to use models -//var ScatterplotModel = BaseModel.extend( LoggableMixin ).extend({ -// logger : console -//}); - +//============================================================================== +/** + * Scatterplot control UI as a backbone view + * + */ var ScatterplotView = BaseView.extend( LoggableMixin ).extend({ //logger : console, tagName : 'form', @@ -370,15 +376,19 @@ }, initialize : function( attributes ){ - if( !attributes.dataset ){ + if( !attributes || !attributes.dataset ){ throw( "ScatterplotView requires a dataset" ); } else { this.dataset = attributes.dataset; } + + // passed from mako helper + //TODO: integrate to galaxyPaths this.apiDatasetsURL = attributes.apiDatasetsURL; + + // set up the basic chart infrastructure with config (if any) this.chartConfig = attributes.chartConfig || {}; this.log( 'this.chartConfig:', this.chartConfig ); - this.plot = new TwoVarScatterplot( this.chartConfig ); }, @@ -422,18 +432,23 @@ }, renderScatterplot : function(){ + // parse the column values for both + // indeces (for the data fetch) and names (for the graph) var view = this, - url = this.apiDatasetsURL + '/' + this.dataset.id + '?data_type=raw_data&'; + url = this.apiDatasetsURL + '/' + this.dataset.id + '?data_type=raw_data&', + xSelector = this.$el.find( '[name="x-column"]' ), xVal = xSelector.val(), xName = xSelector.children( '[value="' + xVal + '"]' ).text(), + ySelector = this.$el.find( '[name="y-column"]' ), yVal = ySelector.val(), yName = ySelector.children( '[value="' + yVal + '"]' ).text(); - //TODO this.log( xName, yName ); + this.chartConfig.xLabel = xName; this.chartConfig.yLabel = yName; + //TODO: alter directly view.plot.updateConfig( this.chartConfig ); @@ -441,6 +456,7 @@ //TODO: other vals: max, start, page //TODO: chart config + // fetch the data, sending chosen columns to the server url += jQuery.param({ columns : '[' + [ xVal, yVal ] + ']' }); @@ -450,6 +466,7 @@ url : url, dataType : 'json', success : function( response ){ + //TODO: server sends back an endpoint, cache for next pagination request view.endpoint = response.endpoint; view.plot.render( // pull apart first two regardless of number of columns @@ -464,3 +481,8 @@ } }); +//============================================================================== +return { + //TwoVarScatterplot : TwoVarScatterplot, + ScatterplotView : ScatterplotView +};}); \ No newline at end of file diff -r 8b7dfceabe3ea6cc15001f05a623157e95f1bcb7 -r 327632b4f9992b2c3f4b9c6f705bed1f4e05914d templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -48,7 +48,17 @@  - ${h.js( 'libs/jquery/jquery', 'libs/json2', 'libs/bootstrap', 'libs/underscore', 'libs/backbone/backbone', 'libs/backbone/backbone-relational', 'libs/handlebars.runtime', 'mvc/ui', 'galaxy.base' )} + ${h.js( + 'libs/jquery/jquery', + 'libs/json2', + 'libs/bootstrap', + 'libs/underscore', + 'libs/backbone/backbone', + 'libs/backbone/backbone-relational', + 'libs/handlebars.runtime', + 'mvc/ui', + 'galaxy.base' + )} <script type="text/javascript"> // Set up needed paths. var galaxy_paths = new GalaxyPaths({ diff -r 8b7dfceabe3ea6cc15001f05a623157e95f1bcb7 -r 327632b4f9992b2c3f4b9c6f705bed1f4e05914d templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -6,25 +6,25 @@ <style type="text/css"> .title { - margin: 0px; + margin: 0px; padding: 8px; background-color: #ebd9b2; border: 2px solid #ebd9b2; } .subtitle { - margin: 0px; + margin: 0px; padding: 0px 8px 8px 16px; background-color: #ebd9b2; - color: white; - font-size: small; + color: white; + font-size: small; } #chart-settings-form { /*from width + margin of chart?*/ - float: right; + float: right; width: 100%; - margin: 0px; + margin: 0px; padding-top: 1em; } @@ -45,80 +45,67 @@ overflow: auto; } -.clear { - clear: both; - margin: 0px; -} - - -svg .chart { - /*shape-rendering: crispEdges;*/ -} - svg .grid-line { - fill: none; - stroke: lightgrey; - stroke-opacity: 0.5; - shape-rendering: crispEdges; - stroke-dasharray: 3, 3; + fill: none; + stroke: lightgrey; + stroke-opacity: 0.5; + shape-rendering: crispEdges; + stroke-dasharray: 3, 3; } svg .axis path, svg .axis line { - fill: none; - stroke: black; - shape-rendering: crispEdges; + fill: none; + stroke: black; + shape-rendering: crispEdges; } svg .axis text { - font-family: sans-serif; - font-size: 12px; + font-family: sans-serif; + font-size: 12px; } - svg .glyph { - stroke: none; - fill: black; - fill-opacity: 0.2; + stroke: none; + fill: black; + fill-opacity: 0.2; } - + </style> - + </%def><%def name="javascripts()"> ${parent.javascripts()} -${h.js( - "libs/underscore", - "libs/backbone/backbone", - "libs/backbone/backbone-relational", - "libs/d3", - "mvc/base-mvc", - "viz/scatterplot" -)} +${h.js( "libs/require" )} <script type="text/javascript"> -$(function() { - var hda = ${h.to_json_string( hda )}, - historyID = '${historyID}' - apiDatasetsURL = "${h.url_for( controller='/api/datasets' )}"; - //?? hmmmm - //kwargs = ${h.to_json_string( kwargs )}; - - var settingsForm = new ScatterplotView({ - dataset : hda, - el : $( '#chart-settings-form' ), +require.config({ baseUrl : "${h.url_for( '/static/scripts' )}", }); + +require([ "viz/scatterplot" ], function( scatterplot ){ + + var hda = ${h.to_json_string( hda )}, + historyID = '${historyID}' + apiDatasetsURL = "${h.url_for( controller='/api/datasets' )}"; + //?? hmmmm + //kwargs = ${h.to_json_string( kwargs )}; + + var settingsForm = new scatterplot.ScatterplotView({ + dataset : hda, + el : $( '#chart-settings-form' ), apiDatasetsURL : apiDatasetsURL, + chartConfig : { containerSelector : '#chart-holder', marginTop : 20, } - }).render(); + }).render(); }); + </script></%def><%def name="body()"><h2 class="title">Scatterplot of '${hda['name']}'</h2><p class="subtitle">${hda['misc_info']}</p> - <div id="chart-holder"></div> - <div id="chart-settings-form"></div> + <div id="chart-holder"></div> + <div id="chart-settings-form"></div></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fix Cuffdiff parameter group naming.
by Bitbucket 23 Sep '12

23 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8b7dfceabe3e/ changeset: 8b7dfceabe3e user: jgoecks date: 2012-09-24 01:34:11 summary: Fix Cuffdiff parameter group naming. affected #: 1 file diff -r 3574c1fa4cb3494f82fd1915c63da6154b230756 -r 8b7dfceabe3ea6cc15001f05a623157e95f1bcb7 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -22,11 +22,11 @@ --cds_diff_output=$cds_diff --promoters_diff_output=$promoters_diff - ## Set paired-end data parameters? - #if $singlePaired.sPaired == "Yes": - -m $singlePaired.frag_mean_len - -s $singlePaired.frag_len_std_dev - #end if + ## Set advanced data parameters? + #if $additional.sAdditional == "Yes": + -m $additional.frag_mean_len + -s $additional.frag_len_std_dev + #end if ## Normalization? #if str($do_normalization) == "Yes": @@ -113,15 +113,15 @@ </when><when value="No"></when></conditional> - <conditional name="singlePaired"> - <param name="sPaired" type="select" label="Set Parameters for Paired-end Reads? (not recommended)"> + <conditional name="additional"> + <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended)"><option value="No">No</option><option value="Yes">Yes</option></param><when value="No"></when><when value="Yes"> - <param name="frag_mean_len" type="integer" value="20" label="Average Fragment Length"/> - <param name="frag_len_std_dev" type="integer" value="20" label="Fragment Length Standard Deviation"/> + <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/> + <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/></when></conditional></inputs> @@ -154,7 +154,7 @@ <param name="min_alignment_count" value="0" /><param name="do_bias_correction" value="No" /><param name="do_normalization" value="No" /> - <param name="sPaired" value="single"/> + <param name="sAdditional" value="No"/><!-- Line diffs are needed because cuffdiff does not produce deterministic output. TODO: can we find datasets that lead to deterministic behavior? 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: fixes to ae57c837ab03
by Bitbucket 21 Sep '12

21 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3574c1fa4cb3/ changeset: 3574c1fa4cb3 user: carlfeberhard date: 2012-09-22 00:39:04 summary: fixes to ae57c837ab03 affected #: 3 files diff -r 45f11c9b4affd9006f1f7159368567cd412d20b8 -r 3574c1fa4cb3494f82fd1915c63da6154b230756 lib/galaxy/visualization/data_providers/basic.py --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -90,7 +90,7 @@ if( skip_comments and start_val == 0 and self.original_dataset.metadata.comment_lines ): - start_val = self.original_dataset.metadata.comment_lines + start_val = int( self.original_dataset.metadata.comment_lines ) + 1 response = {} response[ 'data' ] = data = [] @@ -102,6 +102,8 @@ "column index (%d) must be less" % ( column ) + " than the number of columns: %d" % ( self.original_dataset.metadata.columns ) ) + #print columns, start_val, max_vals, skip_comments, kwargs + # alter meta by column_selectors (if any) def cast_val( val, type ): """ Cast value based on type. """ @@ -125,8 +127,9 @@ fields = line.split() fields_len = len( fields ) #TODO: this will return the wrong number of columns for abberrant lines - data.append([ cast_val( fields[c], self.original_dataset.metadata.column_types[c] ) - for c in columns if ( c < fields_len ) ]) + line_data = [ cast_val( fields[c], self.original_dataset.metadata.column_types[c] ) + for c in columns if ( c < fields_len ) ] + data.append( line_data ) response[ 'endpoint' ] = dict( last_line=( count - 1 ), file_ptr=f.tell() ) f.close() diff -r 45f11c9b4affd9006f1f7159368567cd412d20b8 -r 3574c1fa4cb3494f82fd1915c63da6154b230756 lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -189,13 +189,9 @@ # Return data. data = None data_provider = trans.app.data_provider_registry.get_data_provider( trans, raw=True, original_dataset=dataset ) + print 'data_provider:', data_provider - if data_provider == ColumnDataProvider: - #pre: should have column kwargs - #print 'kwargs:', kwargs - #TODO??: could default to first two here - assert 'cols' in kwargs, ( - "ColumnDataProvider needs a 'cols' parameter in the query string" ) + if isinstance( data_provider, ColumnDataProvider ): data = data_provider.get_data( **kwargs ) else: diff -r 45f11c9b4affd9006f1f7159368567cd412d20b8 -r 3574c1fa4cb3494f82fd1915c63da6154b230756 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -2,22 +2,21 @@ <%def name="stylesheets()"> ${parent.stylesheets()} -##${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom", "library" )} <style type="text/css"> -* { margin: 0px, padding: 0px; } .title { - margin: 0px; + margin: 0px; padding: 8px; background-color: #ebd9b2; + border: 2px solid #ebd9b2; } .subtitle { - margin: 0px; - padding: 0px, 8px, 8px, 16px; + margin: 0px; + padding: 0px 8px 8px 16px; background-color: #ebd9b2; - color: grey; + color: white; font-size: small; } @@ -25,7 +24,7 @@ /*from width + margin of chart?*/ float: right; width: 100%; - background-color: #ebd9b2; + margin: 0px; padding-top: 1em; } 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: Circster: add support for drawing a generic quantitative track and draw summary tree data using a single path.
by Bitbucket 21 Sep '12

21 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/45f11c9b4aff/ changeset: 45f11c9b4aff user: jgoecks date: 2012-09-21 23:44:41 summary: Circster: add support for drawing a generic quantitative track and draw summary tree data using a single path. affected #: 1 file diff -r ae57c837ab039ded7f5056252c2e630988080faf -r 45f11c9b4affd9006f1f7159368567cd412d20b8 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -46,7 +46,7 @@ width = self.$el.width(), height = self.$el.height(), // Compute radius start based on model, will be centered - // and fit entirely inside element by default + // and fit entirely inside element by default. init_radius_start = ( Math.min(width, height)/2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) ); @@ -67,7 +67,7 @@ return utils.is_visible(this, svg); }); visible_elts.each(function(d, i) { - console.log(this.attr('title')); + // TODO: redraw visible elements. }); })) .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") @@ -78,7 +78,9 @@ this.model.get('tracks').each(function(track, index) { var dataset = track.get('genome_wide_data'), radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), - track_renderer_class = (dataset instanceof visualization.GenomeWideBigWigData ? CircsterBigWigTrackRenderer : CircsterSummaryTreeTrackRenderer ); + track_renderer_class = (dataset instanceof visualization.GenomeWideBigWigData ? + CircsterBigWigTrackRenderer : + CircsterSummaryTreeTrackRenderer ); var track_renderer = new track_renderer_class({ track: track, @@ -105,12 +107,12 @@ var genome_arcs = this.chroms_layout(), radius_start = this.options.radius_start, radius_end = this.options.radius_end, - base_arc = svg.append("g").attr("id", "inner-arc"), + track_parent_elt = svg.append("g").attr("id", "inner-arc"), arc_gen = d3.svg.arc() .innerRadius(radius_start) .outerRadius(radius_end), // Draw arcs. - chroms_elts = base_arc.selectAll("#inner-arc>path") + chroms_elts = track_parent_elt.selectAll("#inner-arc>path") .data(genome_arcs).enter().append("path") .attr("d", arc_gen) .style("stroke", "#ccc") @@ -118,12 +120,13 @@ .append("title").text(function(d) { return d.data.chrom; }); // Render data. - this.render_data(svg); + this.render_data(track_parent_elt); + // Apply prefs. var prefs = this.options.track.get('prefs'), block_color = prefs.block_color; if (!block_color) { block_color = prefs.color; } - svg.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); + track_parent_elt.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); }, /** @@ -148,7 +151,7 @@ /** * Render chromosome data and attach elements to svg. */ - render_chrom_data: function(chrom_arc, chrom_data, inner_radius, outer_radius, max) { + render_chrom_data: function(svg, chrom_arc, data, inner_radius, outer_radius, max) { }, /** @@ -167,8 +170,8 @@ // Do dataset layout for each chromosome's data using pie layout. chroms_data_layout = _.map(layout_and_data, function(chrom_info) { var chrom_arc = chrom_info[0], - chrom_data = chrom_info[1]; - return self.render_chrom_data(svg, chrom_arc, chrom_data, + data = chrom_info[1]; + return self.render_chrom_data(svg, chrom_arc, data, r_start, r_end, dataset.get('min'), dataset.get('max')); }); @@ -178,55 +181,15 @@ }); /** - * Layout for summary tree data in a circster visualization. + * Rendered for quantitative data. */ -var CircsterSummaryTreeTrackRenderer = CircsterTrackRenderer.extend({ - - /** - * Returns layouts for drawing a chromosome's data. - */ - render_chrom_data: function(svg, chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { - // FIXME: draw as area: - /* - // If no chrom data, return null. - if (!chrom_data || typeof chrom_data === "string") { - return null; - } - - var data = chrom_data[0], - delta = chrom_data[3], - scale = d3.scale.linear() - .domain( [min, max] ) - .range( [inner_radius, outer_radius] ), - arc_layout = d3.layout.pie().value(function(d) { - return delta; - }) - .startAngle(chrom_arc.startAngle) - .endAngle(chrom_arc.endAngle), - arcs = arc_layout(data); - - // Use scale to assign outer radius. - _.each(data, function(datum, index) { - arcs[index].outerRadius = scale(datum[1]); - }); - - return arcs; - */ - } -}); - -/** - * Layout for BigWig data in a circster visualization. - */ -var CircsterBigWigTrackRenderer = CircsterTrackRenderer.extend({ +var CircsterQuantitativeTrackRenderer = CircsterTrackRenderer.extend({ /** - * Render chromosome data and attach elements to svg. + * Renders quantitative data with the form [x, value] and assumes data is equally spaced across + * chromosome. */ - render_chrom_data: function(svg, chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { - var data = chrom_data.data; - if (data.length === 0) { return; } - + render_quantitative_data: function(svg, chrom_arc, data, inner_radius, outer_radius, min, max) { // Radius scaler. var radius = d3.scale.linear() .domain([min, max]) @@ -237,14 +200,8 @@ .domain([0, data.length]) .range([chrom_arc.startAngle, chrom_arc.endAngle]); - // FIXME: - // *area is not necessary as long as 0 is used as the inner radius. - // *could provide fill as an option. - - // Use both a line and area; area creates definition and line ensures that something is - // always drawn. var line = d3.svg.line.radial() - .interpolate("linear-closed") + .interpolate("linear") .radius(function(d) { return radius(d[1]); }) .angle(function(d, i) { return angle(i); }); @@ -260,12 +217,42 @@ parent.append("path") .attr("class", "chrom-data") .attr("d", area); - - parent.append("path") - .attr("class", "chrom-data") - .attr("d", line); } +}) + +/** + * Layout for summary tree data in a circster visualization. + */ +var CircsterSummaryTreeTrackRenderer = CircsterQuantitativeTrackRenderer.extend({ + + /** + * Renders a chromosome's data. + */ + render_chrom_data: function(svg, chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { + // If no chrom data, return null. + if (!chrom_data || typeof chrom_data === "string") { + return null; + } + + return this.render_quantitative_data(svg, chrom_arc, chrom_data[0], inner_radius, outer_radius, min, max); + } +}); + +/** + * Layout for BigWig data in a circster visualization. + */ +var CircsterBigWigTrackRenderer = CircsterQuantitativeTrackRenderer.extend({ + + /** + * Renders a chromosome's data. + */ + render_chrom_data: function(svg, chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { + var data = chrom_data.data; + if (data.length === 0) { return; } + + return this.render_quantitative_data(svg, chrom_arc, data, inner_radius, outer_radius, min, max); + } }); return { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: fixed(?) weird permissions on jquery-ui; scatterplot: major adjustments;
by Bitbucket 21 Sep '12

21 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ae57c837ab03/ changeset: ae57c837ab03 user: carlfeberhard date: 2012-09-21 22:42:29 summary: fixed(?) weird permissions on jquery-ui; scatterplot: major adjustments; affected #: 8 files diff -r 63a8fb1d8e2b8a8da71a5b618ef65981ff5c4ac3 -r ae57c837ab039ded7f5056252c2e630988080faf lib/galaxy/visualization/data_providers/basic.py --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -45,31 +45,64 @@ """ iterator = self.get_iterator( chrom, start, end ) return self.process_data( iterator, start_val, max_vals, **kwargs ) + def write_data_to_file( self, filename, **kwargs ): """ Write data in region defined by chrom, start, and end to a file. """ raise Exception( "Unimplemented Function" ) + class ColumnDataProvider( BaseDataProvider ): """ Data provider for columnar data """ + MAX_LINES_RETURNED = 30000 - def __init__( self, original_dataset ): + def __init__( self, original_dataset, max_lines_returned=MAX_LINES_RETURNED ): # Compatibility check. if not isinstance( original_dataset.datatype, Tabular ): raise Exception( "Data provider can only be used with tabular data" ) # Attribute init. self.original_dataset = original_dataset + # allow throttling + self.max_lines_returned = max_lines_returned - def get_data( self, cols, start_val=0, max_vals=sys.maxint, **kwargs ): + def get_data( self, columns, start_val=0, max_vals=None, skip_comments=True, **kwargs ): """ Returns data from specified columns in dataset. Format is list of lists where each list is a line of data. """ - - cols = from_json_string( cols ) + #TODO: validate kwargs + try: + max_vals = int( max_vals ) + max_vals = min([ max_vals, self.max_lines_returned ]) + except ( ValueError, TypeError ): + max_vals = self.max_lines_returned + try: + start_val = int( start_val ) + start_val = max([ start_val, 0 ]) + except ( ValueError, TypeError ): + start_val = 0 + + # skip comment lines (if any/avail) + # pre: should have original_dataset and + if( skip_comments + and start_val == 0 + and self.original_dataset.metadata.comment_lines ): + start_val = self.original_dataset.metadata.comment_lines + + response = {} + response[ 'data' ] = data = [] + + #TODO bail if columns None, not parsable, not within meta.columns + # columns is an array of ints for now (should handle column names later) + columns = from_json_string( columns ) + assert( all([ column < self.original_dataset.metadata.columns for column in columns ]) ),( + "column index (%d) must be less" % ( column ) + + " than the number of columns: %d" % ( self.original_dataset.metadata.columns ) ) + + # alter meta by column_selectors (if any) def cast_val( val, type ): """ Cast value based on type. """ if type == 'int': @@ -80,23 +113,23 @@ except: pass return val - data = [] f = open( self.original_dataset.file_name ) + #TODO: add f.seek if given fptr in kwargs for count, line in enumerate( f ): if count < start_val: continue - if max_vals and count-start_val >= max_vals: - message = self.error_max_vals % ( max_vals, "features" ) + + if ( count - start_val ) >= max_vals: break fields = line.split() - #pre: column indeces should be avail in fields - for col_index in cols: - assert col_index < len( fields ), ( - "column index (%d) must be less than fields length: %d" % ( col_index, len( fields ) ) ) - - data.append( [ cast_val( fields[c], self.original_dataset.metadata.column_types[c] ) for c in cols ] ) + fields_len = len( fields ) + #TODO: this will return the wrong number of columns for abberrant lines + data.append([ cast_val( fields[c], self.original_dataset.metadata.column_types[c] ) + for c in columns if ( c < fields_len ) ]) + response[ 'endpoint' ] = dict( last_line=( count - 1 ), file_ptr=f.tell() ) f.close() - - return data + + return response + diff -r 63a8fb1d8e2b8a8da71a5b618ef65981ff5c4ac3 -r ae57c837ab039ded7f5056252c2e630988080faf lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -38,26 +38,27 @@ return str( e ) # Use data type to return particular type of data. - if data_type == 'state': - rval = self._dataset_state( trans, dataset ) - elif data_type == 'converted_datasets_state': - rval = self._converted_datasets_state( trans, dataset, kwd.get( 'chrom', None ) ) - elif data_type == 'data': - rval = self._data( trans, dataset, **kwd ) - elif data_type == 'features': - rval = self._search_features( trans, dataset, kwd.get( 'query ' ) ) - elif data_type == 'raw_data': - rval = self._raw_data( trans, dataset, **kwd ) - elif data_type == 'track_config': - rval = self.get_new_track_config( trans, dataset ) - else: - # Default: return dataset as API value. - try: + try: + if data_type == 'state': + rval = self._dataset_state( trans, dataset ) + elif data_type == 'converted_datasets_state': + rval = self._converted_datasets_state( trans, dataset, kwd.get( 'chrom', None ) ) + elif data_type == 'data': + rval = self._data( trans, dataset, **kwd ) + elif data_type == 'features': + rval = self._search_features( trans, dataset, kwd.get( 'query ' ) ) + elif data_type == 'raw_data': + rval = self._raw_data( trans, dataset, **kwd ) + elif data_type == 'track_config': + rval = self.get_new_track_config( trans, dataset ) + else: + # Default: return dataset as API value. rval = dataset.get_api_value() - except Exception, e: - rval = "Error in dataset API at listing contents" - log.error( rval + ": %s" % str(e) ) - trans.response.status = 500 + + except Exception, e: + rval = "Error in dataset API at listing contents" + log.error( rval + ": %s" % str(e), exc_info=True ) + trans.response.status = 500 return rval def _dataset_state( self, trans, dataset, **kwargs ): diff -r 63a8fb1d8e2b8a8da71a5b618ef65981ff5c4ac3 -r ae57c837ab039ded7f5056252c2e630988080faf lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -800,26 +800,26 @@ return self.get_visualization( trans, id ) @web.expose - def scatterplot( self, trans, dataset_id, cols ): + def scatterplot( self, trans, dataset_id, **kwargs ): # Get HDA. hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - - # get some metadata for the page hda_dict = hda.get_api_value() - #title = "Scatter plot of {name}:".format( **hda_dict ) - #subtitle = "{misc_info}".format( **hda_dict ) + hda_dict[ 'id' ] = dataset_id + if( hda_dict[ 'metadata_column_names' ] == None + and hasattr( hda.datatype, 'column_names' ) ): + hda_dict[ 'metadata_column_names' ] = hda.datatype.column_names + history_id = trans.security.encode_id( hda.history.id ) #TODO: add column data # Read data. - data_provider = ColumnDataProvider( original_dataset=hda ) - data = data_provider.get_data( cols ) + #data_provider = ColumnDataProvider( original_dataset=hda, **kwargs ) + #data = data_provider.get_data() # Return plot. return trans.fill_template_mako( "visualization/scatterplot.mako", - title=hda.name, subtitle=hda.info, - hda=hda, - data=data ) - + hda=hda_dict, + historyID=history_id, + kwargs=kwargs ) @web.json def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ): diff -r 63a8fb1d8e2b8a8da71a5b618ef65981ff5c4ac3 -r ae57c837ab039ded7f5056252c2e630988080faf static/scripts/viz/scatterplot.js --- /dev/null +++ b/static/scripts/viz/scatterplot.js @@ -0,0 +1,466 @@ +/* ============================================================================= +todo: + outside this: + BUG: visualization menu doesn't disappear + BUG?: get column_names (from datatype if necessary) + BUG: single vis in popupmenu should have tooltip with that name NOT 'Visualizations' + + ??: maybe better to do this with a canvas... + + move renderScatter plot to obj, possibly view? + + fix x axis - adjust ticks when tick labels are long - move odds down and extend tick line + + provide callback in view to load data incrementally - for large sets + + paginate + handle rerender + use endpoint (here and on the server (fileptr)) + fetch (new?) data + handle rerender + + selectable list of preset column comparisons (rnaseq etc.) + multiple plots on one page (small multiples) + + where are bad dataprovider params handled? api/datasets? + + config changes to the graph + render stats on the data (max, min, count) + render warning on long data (> maxDataPoints) + adjust endpoint + + loading indicator + + download svg -> base64 encode + dress up ui + + incorporate glyphs, glyph state renderers + + validate columns selection (here or server) + + ?? ensure svg styles thru d3 or css? + d3: configable (easily) + css: standard - better maintenance + ? override at config + +============================================================================= */ +/** + * Two Variable scatterplot visualization using d3 + * Uses semi transparent circles to show density of data in x, y grid + * usage : + * var plot = new TwoVarScatterplot({ containerSelector : 'div#my-plot', ... }) + * plot.render( xColumnData, yColumnData ); + * + * depends on: d3, underscore + */ +function TwoVarScatterplot( config ){ + var plot = this, + GUESS_AT_SVG_CHAR_WIDTH = 10, + GUESS_AT_SVG_CHAR_HEIGHT = 12, + PADDING = 8, + X_LABEL_TOO_LONG_AT = 5; + + //this.debugging = true; + this.log = function(){ + if( this.debugging && console && console.debug ){ + var args = Array.prototype.slice.call( arguments ); + args.unshift( this.toString() ); + console.debug.apply( null, args ); + } + }; + this.log( 'new TwoVarScatterplot:', config ); + + // ........................................................ set up chart config + // config will default to these values when not passed in + //NOTE: called on new + this.defaults = { + id : 'TwoVarScatterplot', + containerSelector : 'body', + maxDataPoints : 30000, + bubbleRadius : 4, + entryAnimDuration : 500, + //TODO: no effect? + xNumTicks : 10, + yNumTicks : 10, + xAxisLabelBumpY : 40, + yAxisLabelBumpX : -35, + width : 500, + height : 500, + //TODO: anyway to make this a sub-obj? + marginTop : 50, + marginRight : 50, + marginBottom : 50, + marginLeft : 50, + xMin : null, + xMax : null, + yMin : null, + yMax : null, + xLabel : "X", + yLabel : "Y" + }; + this.config = _.extend( {}, this.defaults, config ); + + this.updateConfig = function( newConfig ){ + _.extend( this.config, newConfig ); + }; + + // ........................................................ helpers + this.toString = function(){ + return this.config.id; + }; + this.translateStr = function( x, y ){ + return 'translate(' + x + ',' + y + ')'; + }; + this.rotateStr = function( d, x, y ){ + return 'rotate(' + d + ',' + x + ',' + y + ')'; + }; + + // ........................................................ initial element creation + //NOTE: called on new + this.svg = d3.select( this.config.containerSelector ) + .append( "svg:svg" ).attr( "class", "chart" ).style( 'display', 'none' ); + this.content = this.svg.append( "svg:g" ).attr( "class", "content" ); + + this.xAxis = this.content.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'x-axis' ); + this.xAxisLabel = this.xAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'x-axis-label' ); + + 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.adjustChartDimensions = function(){ + this.svg + .attr( "width", this.config.width + ( this.config.marginRight + this.config.marginLeft ) ) + .attr( "height", this.config.height + ( this.config.marginTop + this.config.marginBottom ) ) + // initial is hidden - show it + .style( 'display', 'block' ); + + // move content group away from margins + this.content = this.svg.select( "g.content" ) + .attr( "transform", this.translateStr( this.config.marginLeft, this.config.marginTop ) ); + }; + + // ........................................................ data and scales + this.preprocessData = function( data ){ + // set a cap on the data, limit to first n points + return data.slice( 0, this.config.maxDataPoints ); + }; + + this.setUpDomains = function( xCol, yCol ){ + this.xMin = this.config.xMin || d3.min( xCol ); + this.xMax = this.config.xMax || d3.max( xCol ); + this.yMin = this.config.yMin || d3.min( yCol ); + this.yMax = this.config.yMax || d3.max( yCol ); + }; + + this.setUpScales = function(){ + // Interpolation for x, y based on data domains + this.xScale = d3.scale.linear() + .domain([ this.xMin, this.xMax ]) + .range([ 0, this.config.width ]), + this.yScale = d3.scale.linear() + .domain([ this.yMin, this.yMax ]) + .range([ this.config.height, 0 ]); + }; + + // ........................................................ axis and ticks + this.setUpXAxis = function(){ + // origin: bottom, left + //TODO: incoporate top, right + this.xAxisFn = d3.svg.axis() + .scale( this.xScale ) + .ticks( this.config.xNumTicks ) + .orient( 'bottom' ); + this.xAxis// = content.select( 'g#x-axis' ) + .attr( 'transform', this.translateStr( 0, this.config.height ) ) + .call( this.xAxisFn ); + this.log( 'xAxis:', this.xAxis ); + + //TODO: this isn't reliable with -/+ ranges - better to go thru each tick + this.xLongestLabel = d3.max( _.map( [ this.xMin, this.xMax ], + function( number ){ return ( String( number ) ).length; } ) ); + this.log( 'xLongestLabel:', this.xLongestLabel ); + + if( this.xLongestLabel >= X_LABEL_TOO_LONG_AT ){ + //TODO: adjust ticks when tick labels are long - move odds down and extend tick line + // (for now) hide them + this.xAxis.selectAll( 'g' ).filter( ':nth-child(odd)' ).style( 'display', 'none' ); + } + + this.xAxisLabel// = xAxis.select( 'text#x-axis-label' ) + .attr( 'x', this.config.width / 2 ) + .attr( 'y', this.config.xAxisLabelBumpY ) + .attr( 'text-anchor', 'middle' ) + .text( this.config.xLabel ); + this.log( 'xAxisLabel:', this.xAxisLabel ); + }; + + this.setUpYAxis = function(){ + 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.yLongestLabel = d3.max( _.map( [ this.yMin, this.yMax ], + function( number ){ return ( String( number ) ).length; } ) ); + this.log( 'yLongestLabel:', this.yLongestLabel ); + + //TODO: ugh ... so clumsy + //TODO: this isn't reliable with -/+ ranges - better to go thru each tick + var neededY = this.yLongestLabel * GUESS_AT_SVG_CHAR_WIDTH + ( PADDING ); + + // increase width for xLongerStr, increase margin for y + //TODO??: (or transform each number: 2k) + if( this.config.yAxisLabelBumpX > -( neededY ) ){ + this.config.yAxisLabelBumpX = -( neededY ); + } + if( this.config.marginLeft < neededY ){ + this.config.marginLeft = neededY + GUESS_AT_SVG_CHAR_HEIGHT; + // update dimensions, translations + this.adjustChartDimensions(); + } + this.log( 'this.config.yAxisLableBumpx, this.config.marginLeft:', + this.config.yAxisLabelBumpX, this.config.marginLeft ); + + this.yAxisLabel// = yAxis.select( 'text#y-axis-label' ) + .attr( 'x', this.config.yAxisLabelBumpX ) + .attr( 'y', this.config.height / 2 ) + .attr( 'text-anchor', 'middle' ) + .attr( 'transform', this.rotateStr( -90, this.config.yAxisLabelBumpX, this.config.height / 2 ) ) + .text( this.config.yLabel ); + this.log( 'yAxisLabel:', this.yAxisLabel ); + }; + + // ........................................................ grid lines + this.renderGrid = function(){ + // VERTICAL + // select existing + this.vGridLines = this.content.selectAll( 'line.v-grid-line' ) + .data( this.xScale.ticks( this.xAxisFn.ticks()[0] ) ); + + // append any extra lines needed (more ticks) + this.vGridLines.enter().append( 'svg:line' ) + .classed( 'grid-line v-grid-line', true ); + + // update the attributes of existing and appended + this.vGridLines + .attr( 'x1', this.xScale ) + .attr( 'y1', 0 ) + .attr( 'x2', this.xScale ) + .attr( 'y2', this.config.height ); + + // remove unneeded (less ticks) + this.vGridLines.exit().remove(); + this.log( 'vGridLines:', this.vGridLines ); + + // HORIZONTAL + this.hGridLines = this.content.selectAll( 'line.h-grid-line' ) + .data( this.yScale.ticks( this.yAxisFn.ticks()[0] ) ); + + this.hGridLines.enter().append( 'svg:line' ) + .classed( 'grid-line h-grid-line', true ); + + this.hGridLines + .attr( 'x1', 0 ) + .attr( 'y1', this.yScale ) + .attr( 'x2', this.config.width ) + .attr( 'y2', this.yScale ); + + this.hGridLines.exit().remove(); + this.log( 'hGridLines:', this.hGridLines ); + }; + + // ........................................................ data points + //TODO: these to config ...somehow + //TODO: use these in renderDatapoints ...somehow + this.glyphEnterState = function( d3Elem ){ + + }; + this.glyphFinalState = function( d3Elem ){ + + }; + this.glyphExitState = function( d3Elem ){ + + }; + + this.renderDatapoints = function( xCol, yCol ){ + + var xPosFn = function( d, i ){ + return plot.xScale( xCol[ i ] ); + }; + var yPosFn = function( d, i ){ + return plot.yScale( yCol[ i ] ); + }; + + // select all existing glyphs and compare to incoming data + // enter() will yield those glyphs that need to be added + // exit() will yield existing glyphs that need to be removed + this.datapoints = this.content.selectAll( ".glyph" ) + .data( xCol ); + + // enter - new data to be added as glyphs: give them a 'entry' position and style + this.datapoints.enter() + .append( "svg:circle" ).attr( "class", "glyph" ) + // start all bubbles at corner... + .attr( "cx", xPosFn ) + .attr( "cy", 0 ) + .attr( "r", 0 ); + + // for all existing glyphs and those that need to be added: transition anim to final state + this.datapoints + // ...animate to final position + .transition().duration( this.config.entryAnimDuration ) + .attr( "cx", xPosFn ) + .attr( "cy", yPosFn ) + .attr( "r", this.config.bubbleRadius ); + + // glyphs that need to be removed: transition to from normal state to 'exit' state, remove from DOM + this.datapoints.exit() + .transition().duration( this.config.entryAnimDuration ) + .attr( "cy", this.config.height ) + .attr( "r", 0 ) + .style( "fill-opacity", 0 ) + .remove(); + + this.log( this.datapoints, 'glyphs rendered' ); + }; + + this.render = function( xCol, yCol ){ + //pre: columns passed are numeric + this.log( 'renderScatterplot', xCol.length, yCol.length, this.config ); + + //pre: xCol.len == yCol.len + //TODO: ^^ isn't necessarily true with current ColumnDataProvider + xCol = this.preprocessData( xCol ); + yCol = this.preprocessData( yCol ); + this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); + + //TODO: compute min, max on server. + this.setUpDomains( xCol, yCol ); + this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); + + this.setUpScales(); + this.adjustChartDimensions(); + + this.setUpXAxis(); + this.setUpYAxis(); + + this.renderGrid(); + this.renderDatapoints( xCol, yCol ); + //TODO: on hover red line to axes, display values + }; +} + +//// ugh...this seems like the wrong way to use models +//var ScatterplotModel = BaseModel.extend( LoggableMixin ).extend({ +// logger : console +//}); + +var ScatterplotView = BaseView.extend( LoggableMixin ).extend({ + //logger : console, + tagName : 'form', + className : 'scatterplot-settings-form', + + events : { + 'click #render-button' : 'renderScatterplot' + }, + + initialize : function( attributes ){ + if( !attributes.dataset ){ + throw( "ScatterplotView requires a dataset" ); + } else { + this.dataset = attributes.dataset; + } + this.apiDatasetsURL = attributes.apiDatasetsURL; + this.chartConfig = attributes.chartConfig || {}; + this.log( 'this.chartConfig:', this.chartConfig ); + + this.plot = new TwoVarScatterplot( this.chartConfig ); + }, + + render : function(){ + //TODO: to template + var view = this, + html = '', + columnHtml = ''; + // build column select controls for each x, y (based on name if available) + // ugh...hafta preprocess + this.dataset.metadata_column_types = this.dataset.metadata_column_types.split( ', ' ); + _.each( this.dataset.metadata_column_types, function( type, index ){ + // use only numeric columns + if( type === 'int' || type === 'float' ){ + var name = 'column ' + index; + // label with the name if available + if( view.dataset.metadata_column_names ){ + name = view.dataset.metadata_column_names[ index ]; + } + columnHtml += '<option value="' + index + '">' + name + '</column>'; + } + }); + + // column selector containers + html += '<div id="x-column-input">'; + html += '<label for="">Data column for X: </label><select name="x-column">' + columnHtml + '</select>'; + html += '</div>'; + + html += '<div id="y-column-input">'; + html += '<label for="">Data column for Y: </label><select name="y-column">' + columnHtml + '</select>'; + html += '</div>'; + + html += '<input id="render-button" type="button" value="Draw" />'; + html += '<div class="clear"></div>'; + + //TODO: other vals: max_vals, start_val, pagination + + this.$el.append( html ); + this.$el.find( '#render-button' ); + return this; + }, + + renderScatterplot : function(){ + var view = this, + url = this.apiDatasetsURL + '/' + this.dataset.id + '?data_type=raw_data&'; + xSelector = this.$el.find( '[name="x-column"]' ), + xVal = xSelector.val(), + xName = xSelector.children( '[value="' + xVal + '"]' ).text(), + ySelector = this.$el.find( '[name="y-column"]' ), + yVal = ySelector.val(), + yName = ySelector.children( '[value="' + yVal + '"]' ).text(); + //TODO + this.log( xName, yName ); + this.chartConfig.xLabel = xName; + this.chartConfig.yLabel = yName; + //TODO: alter directly + view.plot.updateConfig( this.chartConfig ); + + //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 + + url += jQuery.param({ + columns : '[' + [ xVal, yVal ] + ']' + }); + this.log( 'url:', url ); + + jQuery.ajax({ + url : url, + dataType : 'json', + success : function( response ){ + view.endpoint = response.endpoint; + view.plot.render( + // pull apart first two regardless of number of columns + _.map( response.data, function( columns ){ return columns[0]; } ), + _.map( response.data, function( columns ){ return columns[1]; } ) + ); + }, + error : function( xhr, status, error ){ + alert( 'ERROR:' + status + '\n' + error ); + } + }); + } +}); + diff -r 63a8fb1d8e2b8a8da71a5b618ef65981ff5c4ac3 -r ae57c837ab039ded7f5056252c2e630988080faf templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -194,6 +194,17 @@ }; }; +function create_scatterplot_action_fn( url, params ){ + action = function() { + var galaxy_main = $( window.parent.document ).find( 'iframe#galaxy_main' ), + final_url = url + '/scatterplot?' + $.param(params); + galaxy_main.attr( 'src', final_url ); + $( 'div.popmenu-wrapper' ).remove(); + return false; + }; + return action; +} + /** * Create popup menu for visualization icon. */ @@ -208,14 +219,20 @@ // Create visualization action. create_viz_action = function(visualization) { var action; - if (visualization === 'trackster') { - action = create_trackster_action_fn(vis_url, params, dbkey); - } - else { - action = function() { - window.parent.location = vis_url + '/' + visualization + '?' + - $.param(params); - }; + switch( visualization ){ + + case 'trackster': + action = create_trackster_action_fn(vis_url, params, dbkey); + break; + + case 'scatterplot': + action = create_scatterplot_action_fn( vis_url, params ); + break; + + default: + action = function(){ + window.parent.location = vis_url + '/' + visualization + '?' + $.param(params); + } } return action; }, @@ -234,6 +251,7 @@ // Set up action or menu. if (visualizations.length === 1) { // No need for popup menu because there's a single visualization. + icon.attr( 'title', visualizations[0] ); icon.click(create_viz_action(visualizations[0])); } else { diff -r 63a8fb1d8e2b8a8da71a5b618ef65981ff5c4ac3 -r ae57c837ab039ded7f5056252c2e630988080faf templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -230,10 +230,10 @@ ## information--URL base, dataset id, dbkey, visualizations--in anchor. <% visualizations = data.get_visualizations() - ## HACK: if there are visualizations, only provide trackster for now since others - ## are not ready. + ## HACK: if there are visualizations, only provide trackster for now + ## since others are not ready. - comment out to see all WIP visualizations if visualizations: - visualizations = [ 'trackster' ] + visualizations = [ vis for vis in visualizations if vis in [ 'trackster' ] ] %> %if visualizations: <a href="${h.url_for( controller='visualization' )}" diff -r 63a8fb1d8e2b8a8da71a5b618ef65981ff5c4ac3 -r ae57c837ab039ded7f5056252c2e630988080faf templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -2,23 +2,61 @@ <%def name="stylesheets()"> ${parent.stylesheets()} -${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom", "library" )} +##${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom", "library" )} <style type="text/css"> * { margin: 0px, padding: 0px; } +.title { + margin: 0px; + padding: 8px; + background-color: #ebd9b2; +} + .subtitle { - margin-left: 1em; - margin-top: -1em; + margin: 0px; + padding: 0px, 8px, 8px, 16px; + background-color: #ebd9b2; color: grey; font-size: small; } -.chart { +#chart-settings-form { + /*from width + margin of chart?*/ + float: right; + width: 100%; + background-color: #ebd9b2; + padding-top: 1em; +} + +#chart-settings-form > * { + margin: 8px; +} + +#chart-settings-form input, #chart-settings-form select { + width: 30%; + max-width: 256px; +} + +#chart-settings-form [value=Draw] { + float: right; +} + +#chart-holder { + overflow: auto; +} + +.clear { + clear: both; + margin: 0px; +} + + +svg .chart { /*shape-rendering: crispEdges;*/ } -.grid-line { +svg .grid-line { fill: none; stroke: lightgrey; stroke-opacity: 0.5; @@ -26,18 +64,18 @@ stroke-dasharray: 3, 3; } -.axis path, .axis line { +svg .axis path, svg .axis line { fill: none; stroke: black; shape-rendering: crispEdges; } -.axis text { +svg .axis text { font-family: sans-serif; font-size: 12px; } -circle.bubble { +svg .glyph { stroke: none; fill: black; fill-opacity: 0.2; @@ -49,156 +87,39 @@ <%def name="javascripts()"> ${parent.javascripts()} -${h.js( "libs/d3" )} +${h.js( + "libs/underscore", + "libs/backbone/backbone", + "libs/backbone/backbone-relational", + "libs/d3", + "mvc/base-mvc", + "viz/scatterplot" +)} <script type="text/javascript"> -/* ============================================================================= -todo: - validate columns (here or server) - send: type, column title/name in JSON - - move to obj, possibly view? - fetch (new?) data - config changes to the graph - download svg (png?) - -============================================================================= */ -function translateStr( x, y ){ - return 'translate(' + x + ',' + y + ')'; -} -function rotateStr( d, x, y ){ - return 'rotate(' + d + ',' + x + ',' + y + ')'; -} - $(function() { - // Constants - var data = ${data}, - MAX_DATA_POINTS = 30000, - BUBBLE_RADIUS = 5, - ENTRY_ANIM_DURATION = 500, - X_TICKS = 10, Y_TICKS = 10, - X_AXIS_LABEL_BUMP_Y = 40, - Y_AXIS_LABEL_BUMP_X = -35, - WIDTH = 300, - HEIGHT = 300, - MARGIN= 50, - xLabel = "Magnitude", - yLabel = "Depth"; - - // set a cap on the data, limit to first n points - data = data.slice( 0, MAX_DATA_POINTS ); + var hda = ${h.to_json_string( hda )}, + historyID = '${historyID}' + apiDatasetsURL = "${h.url_for( controller='/api/datasets' )}"; + //?? hmmmm + //kwargs = ${h.to_json_string( kwargs )}; - // split the data into columns - //TODO: compute min, max on server. - var col1_data = data.map( function(e) { return e[0] }), - col2_data = data.map( function(e) { return e[1] }), - xMin = d3.min( col1_data ), - xMax = d3.max( col1_data ), - yMin = d3.min( col2_data ), - yMax = d3.max( col2_data ); - //console.log( 'col1_data:', col1_data ); - //console.log( 'col2_data:', col2_data ); - //console.log( 'xMin, xMax, yMin, yMax:', xMin, xMax, yMin, yMax ); - - // Set up. - d3.select( "body" ).append( "svg:svg" ) - .attr( "width", WIDTH + ( MARGIN * 2 ) ) - .attr( "height", HEIGHT + ( MARGIN * 2 ) ) - .attr( "class", "chart" ); - - // Scale for x, y based on data domains - // origin: bottom, left - var x_scale = d3.scale.linear() - .domain([ xMin, xMax ]) - .range([ 0, WIDTH ]), - y_scale = d3.scale.linear() - .domain([ yMin, yMax ]) - .range([ HEIGHT, 0 ]); - - // Selection of SVG, append group (will group our entire chart), give attributes - // apply a group and transform all coords away from margins - var chart = d3.select( ".chart" ).append( "svg:g" ) - .attr( "class", "content" ) - .attr( "transform", translateStr( MARGIN, MARGIN ) ); - - // axes - var xAxisFn = d3.svg.axis() - .scale( x_scale ) - .ticks( X_TICKS ) - .orient( 'bottom' ); - var xAxis = chart.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'x-axis' ) - .attr( 'transform', translateStr( 0, HEIGHT ) ) - .call( xAxisFn ) - //console.debug( 'xAxis:', xAxis ); window.xAxis = xAxis, window.xAxisFn = xAxisFn; - - var xAxisLabel = xAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'x-axis-label' ) - .attr( 'x', WIDTH / 2 ) - .attr( 'y', X_AXIS_LABEL_BUMP_Y ) - .attr( 'text-anchor', 'middle' ) - .text( xLabel ); - //console.debug( 'xAxisLabel:', xAxisLabel ); window.xAxisLabel = xAxisLabel; - - var yAxisFn = d3.svg.axis() - .scale( y_scale ) - .ticks( Y_TICKS ) - .orient( 'left' ); - var yAxis = chart.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'y-axis' ) - .call( yAxisFn ); - //console.debug( 'yAxis:', yAxis ); window.yAxis = yAxis, window.yAxisFn = yAxisFn; - - var yAxisLabel = yAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'y-axis-label' ) - .attr( 'x', Y_AXIS_LABEL_BUMP_X ) - .attr( 'y', HEIGHT / 2 ) - .attr( 'text-anchor', 'middle' ) - .attr( 'transform', rotateStr( -90, Y_AXIS_LABEL_BUMP_X, HEIGHT / 2 ) ) - .text( yLabel ); - //console.debug( 'yAxisLabel:', yAxisLabel ); window.yAxisLabel = yAxisLabel; - - // grid lines - var hGridLines = chart.selectAll( '.h-grid-line' ) - .data( x_scale.ticks( xAxisFn.ticks()[0] ) ) - .enter().append( 'svg:line' ) - .classed( 'grid-line h-grid-line', true ) - .attr( 'x1', x_scale ).attr( 'y1', 0 ) - .attr( 'x2', x_scale ).attr( 'y2', HEIGHT ) - //console.debug( 'hGridLines:', hGridLines ); window.hGridLines = hGridLines; - - var vGridLines = chart.selectAll( '.v-grid-line' ) - .data( y_scale.ticks( yAxisFn.ticks()[0] ) ) - .enter().append( 'svg:line' ) - .classed( 'grid-line v-grid-line', true ) - .attr( 'x1', 0 ) .attr( 'y1', y_scale ) - .attr( 'x2', WIDTH ).attr( 'y2', y_scale ) - //console.debug( 'vGridLines:', vGridLines ); window.vGridLines = vGridLines; - - // Functions used to render plot. - var xPosFn = function( d, i ){ - return x_scale( col1_data[ i ] ); - }; - var yPosFn = function( d, i ){ - return y_scale( col2_data[ i ] ); - }; - - // Create bubbles for each data point. - chart.selectAll( "circle.bubble" ) - .data(data).enter() - .append( "svg:circle" ).attr( "class", "bubble" ) - // start all bubbles at corner... - .attr( "r", 0 ) - .attr( "fill", "white" ) - // ...animate to final position - .transition().duration( ENTRY_ANIM_DURATION ) - .attr("cx", xPosFn ) - .attr("cy", yPosFn ) - .attr("r", BUBBLE_RADIUS); - - //TODO: on hover red line to axes, display values + var settingsForm = new ScatterplotView({ + dataset : hda, + el : $( '#chart-settings-form' ), + apiDatasetsURL : apiDatasetsURL, + chartConfig : { + containerSelector : '#chart-holder', + marginTop : 20, + } + }).render(); }); </script></%def><%def name="body()"> - <h1 class="title">Scatterplot of '${title}':</h1> - <h2 class="subtitle">${subtitle}</h2> - + <h2 class="title">Scatterplot of '${hda['name']}'</h2> + <p class="subtitle">${hda['misc_info']}</p> + <div id="chart-holder"></div> + <div id="chart-settings-form"></div></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Small additions based on bdd35af2a18a
by Bitbucket 21 Sep '12

21 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/63a8fb1d8e2b/ changeset: 63a8fb1d8e2b user: jgoecks date: 2012-09-21 20:05:37 summary: Small additions based on bdd35af2a18a affected #: 2 files diff -r bdd35af2a18afde11396fcf919b5fb4cacc986ff -r 63a8fb1d8e2b8a8da71a5b618ef65981ff5c4ac3 lib/galaxy/visualization/data_providers/registry.py --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -30,7 +30,8 @@ def get_data_provider( self, trans, name=None, source='data', raw=False, original_dataset=None ): """ - Returns data provider class by name and/or original dataset. + Returns data provider matching parameter values. For standalone data + sources, source parameter is ignored. """ data_provider = None diff -r bdd35af2a18afde11396fcf919b5fb4cacc986ff -r 63a8fb1d8e2b8a8da71a5b618ef65981ff5c4ac3 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -756,15 +756,9 @@ # Get dataset and indexed datatype. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) data_sources = dataset.get_datasources( trans ) - data_provider_registry = trans.app.data_provider_registry - if 'data_standalone' in data_sources: - indexed_type = data_sources['data_standalone']['name'] - data_provider = data_provider_registry.get_data_provider( indexed_type )( dataset ) - else: - indexed_type = data_sources['index']['name'] - # Get converted dataset and append track's genome data. - converted_dataset = dataset.get_converted_dataset( trans, indexed_type ) - data_provider = data_provider_registry.get_data_provider( indexed_type )( converted_dataset, dataset ) + data_provider = trans.app.data_provider_registry.get_data_provider( trans, + original_dataset=dataset, + source='index' ) # HACK: pass in additional params, which are only used for summary tree data, not BBI data. track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) } 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: Viz framework: (a) push data provider creation to registry to simplify provider creation; (b) fix bugs in filters module naming; (c) enable deeper sampling in BBI data provider.
by Bitbucket 21 Sep '12

21 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bdd35af2a18a/ changeset: bdd35af2a18a user: jgoecks date: 2012-09-21 20:00:09 summary: Viz framework: (a) push data provider creation to registry to simplify provider creation; (b) fix bugs in filters module naming; (c) enable deeper sampling in BBI data provider. affected #: 8 files diff -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 -r bdd35af2a18afde11396fcf919b5fb4cacc986ff lib/galaxy/visualization/data_providers/basic.py --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -100,62 +100,3 @@ f.close() return data - -class DataProviderRegistry( object ): - """ - Registry for data providers that enables listing and lookup. - """ - - def __init__( self ): - # Mapping from dataset type name to a class that can fetch data from a file of that - # type. First key is converted dataset type; if result is another dict, second key - # is original dataset type. TODO: This needs to be more flexible. - self.dataset_type_name_to_data_provider = { - "tabix": { - Vcf: VcfTabixDataProvider, - Bed: BedTabixDataProvider, - Gtf: GtfTabixDataProvider, - ENCODEPeak: ENCODEPeakTabixDataProvider, - Interval: IntervalTabixDataProvider, - ChromatinInteractions: ChromatinInteractionsTabixDataProvider, - "default" : TabixDataProvider - }, - "interval_index": IntervalIndexDataProvider, - "bai": BamDataProvider, - "bam": SamDataProvider, - "summary_tree": SummaryTreeDataProvider, - "bigwig": BigWigDataProvider, - "bigbed": BigBedDataProvider - } - - def get_data_provider( name=None, original_dataset=None ): - """ - Returns data provider class by name and/or original dataset. - """ - data_provider = None - if name: - value = dataset_type_name_to_data_provider[ name ] - if isinstance( value, dict ): - # Get converter by dataset extension; if there is no data provider, - # get the default. - data_provider = value.get( original_dataset.datatype.__class__, value.get( "default" ) ) - else: - data_provider = value - elif original_dataset: - # Look up data provider from datatype's informaton. - try: - # Get data provider mapping and data provider for 'data'. If - # provider available, use it; otherwise use generic provider. - _ , data_provider_mapping = original_dataset.datatype.get_track_type() - if 'data_standalone' in data_provider_mapping: - data_provider_name = data_provider_mapping[ 'data_standalone' ] - else: - data_provider_name = data_provider_mapping[ 'data' ] - if data_provider_name: - data_provider = self.get_data_provider( name=data_provider_name, original_dataset=original_dataset ) - else: - data_provider = GenomeDataProvider - except: - pass - return data_provider - \ No newline at end of file diff -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 -r bdd35af2a18afde11396fcf919b5fb4cacc986ff lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -112,6 +112,8 @@ class GenomeDataProvider( BaseDataProvider ): """ Base class for genome data providers. """ + + data_type = None """ Mapping from column name to payload data; this mapping is used to create @@ -314,6 +316,8 @@ class TabixDataProvider( FilterableMixin, GenomeDataProvider ): + data_type = 'tabix' + """ Tabix index data provider for the Galaxy track browser. """ @@ -354,8 +358,10 @@ # class IntervalDataProvider( GenomeDataProvider ): + data_type = 'interval_index' + """ - Processes BED data from native format to payload format. + Processes interval data from native format to payload format. Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ @@ -437,6 +443,8 @@ Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ + + data_type = 'interval_index' def get_iterator( self, chrom, start, end ): raise Exception( "Unimplemented Method" ) @@ -533,6 +541,8 @@ for large datasets. """ + data_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() @@ -570,6 +580,8 @@ """ col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } + + data_type = 'bai' def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): """ @@ -675,6 +687,8 @@ for large datasets. """ + data_type = 'tabix' + def get_iterator( self, chrom, start, end ): # Read first line in order to match chrom naming format. line = source.readline() @@ -706,6 +720,8 @@ """ Summary tree data provider for the Galaxy track browser. """ + + data_type = 'summary_tree' CACHE = LRUCache( 20 ) # Store 20 recently accessed indices for performance @@ -771,6 +787,8 @@ Provides access to intervals from a sorted indexed BAM file. Position data is reported in 1-based, closed format, i.e. SAM/BAM format. """ + + data_type = 'bai' def get_filters( self ): """ @@ -951,6 +969,8 @@ return { 'data': results, 'message': message, 'max_low': max_low, 'max_high': max_high } class SamDataProvider( BamDataProvider ): + + data_type = 'bai' def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None ): """ Create SamDataProvider. """ @@ -966,6 +986,9 @@ """ BBI data provider for the Galaxy track browser. """ + + data_type = 'bigwig' + def valid_chroms( self ): # No way to return this info as of now return None @@ -976,7 +999,7 @@ f.close() return all_dat is not None - def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=None, num_samples=1000, **kwargs ): # Bigwig can be a standalone bigwig file, in which case we use # original_dataset, or coming from wig->bigwig conversion in # which we use converted_dataset @@ -1009,14 +1032,11 @@ return dict( data=dict( min=min, max=max, mean=mean, sd=sd ) ) - # Sample from region using approximately this many samples. - N = 1000 - def summarize_region( bbi, chrom, start, end, num_points ): ''' Returns results from summarizing a region using num_points. NOTE: num_points cannot be greater than end - start or BBI - will return None for all positions.s + will return None for all positions. ''' result = [] @@ -1042,7 +1062,8 @@ return result # Approach is different depending on region size. - if end - start < N: + num_samples = int( num_samples ) + if end - start < num_samples: # Get values for individual bases in region, including start and end. # To do this, need to increase end to next base and request number of points. num_points = end - start + 1 @@ -1050,10 +1071,10 @@ else: # # The goal is to sample the region between start and end uniformly - # using ~N data points. The challenge is that the size of sampled - # intervals rarely is full bases, so sampling using N points will - # leave the end of the region unsampled due to remainders for each - # interval. To recitify this, a new N is calculated based on the + # using ~N (num_samples) data points. The challenge is that the size of + # sampled intervals rarely is full bases, so sampling using N points + # will leave the end of the region unsampled due to remainders for + # each interval. To recitify this, a new N is calculated based on the # step size that covers as much of the region as possible. # # However, this still leaves some of the region unsampled. This @@ -1063,7 +1084,7 @@ # # Start with N samples. - num_points = N + num_points = num_samples step_size = ( end - start ) / num_points # Add additional points to sample in the remainder not covered by # the initial N samples. @@ -1100,6 +1121,8 @@ Interval index files used only for GFF files. """ col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } + + data_type = 'interval_index' def write_data_to_file( self, regions, filename ): source = open( self.original_dataset.file_name ) @@ -1177,6 +1200,8 @@ NOTE: this data provider does not use indices, and hence will be very slow for large datasets. """ + + data_type = 'interval_index' def get_iterator( self, chrom, start, end ): """ diff -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 -r bdd35af2a18afde11396fcf919b5fb4cacc986ff lib/galaxy/visualization/data_providers/registry.py --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -28,46 +28,63 @@ "bigbed": BigBedDataProvider } - def get_data_provider( self, name=None, raw=False, original_dataset=None ): + def get_data_provider( self, trans, name=None, source='data', raw=False, original_dataset=None ): """ Returns data provider class by name and/or original dataset. """ - # If getting raw data, use original dataset type to get data provider. + data_provider = None if raw: + # Working with raw data. if isinstance( original_dataset.datatype, Gff ): - return RawGFFDataProvider + data_provider_class = RawGFFDataProvider elif isinstance( original_dataset.datatype, Bed ): - return RawBedDataProvider + data_provider_class = RawBedDataProvider elif isinstance( original_dataset.datatype, Vcf ): - return RawVcfDataProvider + data_provider_class = RawVcfDataProvider elif isinstance( original_dataset.datatype, Tabular ): - return ColumnDataProvider + data_provider_class = ColumnDataProvider - # Using converted dataset, so get corrsponding data provider. - data_provider = None - if name: - value = self.dataset_type_name_to_data_provider[ name ] - if isinstance( value, dict ): - # Get converter by dataset extension; if there is no data provider, - # get the default. - data_provider = value.get( original_dataset.datatype.__class__, value.get( "default" ) ) - else: - data_provider = value - elif original_dataset: - # Look up data provider from datatype's informaton. - try: - # Get data provider mapping and data provider for 'data'. If - # provider available, use it; otherwise use generic provider. + data_provider = data_provider_class( original_dataset=original_dataset ) + + else: + # Working with converted or standalone dataset. + + if name: + # Provider requested by name; get from mappings. + value = self.dataset_type_name_to_data_provider[ name ] + if isinstance( value, dict ): + # Get converter by dataset extension; if there is no data provider, + # get the default. + data_provider_class = value.get( original_dataset.datatype.__class__, value.get( "default" ) ) + else: + data_provider_class = value + + # If name is the same as original dataset's type, dataset is standalone. + # Otherwise, a converted dataset is being used. + if name == original_dataset.ext: + data_provider = data_provider_class( original_dataset=original_dataset ) + else: + converted_dataset = original_dataset.get_converted_dataset( trans, name ) + deps = original_dataset.get_converted_dataset_deps( trans, name ) + data_provider = data_provider_class( original_dataset=original_dataset, + converted_dataset=converted_dataset, + dependencies=deps ) + + elif original_dataset: + # No name, so look up a provider name from datatype's information. + + # Dataset must have get_track_type function to get data. + if not hasattr( original_dataset.datatype, 'get_track_type'): + return None + + # Get data provider mapping and data provider. _ , data_provider_mapping = original_dataset.datatype.get_track_type() if 'data_standalone' in data_provider_mapping: data_provider_name = data_provider_mapping[ 'data_standalone' ] else: - data_provider_name = data_provider_mapping[ 'data' ] - if data_provider_name: - data_provider = self.get_data_provider( name=data_provider_name, original_dataset=original_dataset ) - else: - data_provider = GenomeDataProvider - except: - pass + data_provider_name = data_provider_mapping[ source ] + + data_provider = self.get_data_provider( trans, name=data_provider_name, original_dataset=original_dataset ) + return data_provider \ No newline at end of file diff -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 -r bdd35af2a18afde11396fcf919b5fb4cacc986ff lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -86,28 +86,14 @@ if msg: return msg - # NOTE: finding valid chroms is prohibitive for large summary trees and is not currently used by - # the client. - valid_chroms = None # Check for data in the genome window. data_provider_registry = trans.app.data_provider_registry - if data_sources.get( 'index' ): - tracks_dataset_type = data_sources['index']['name'] - converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) - indexer = data_provider_registry.get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) - if not indexer.has_data( chrom ): - return messages.NO_DATA - #valid_chroms = indexer.valid_chroms() - else: - # Standalone data provider - standalone_provider = data_provider_registry.get_data_provider( data_sources['data_standalone']['name'] )( dataset ) - kwargs = {"stats": True} - if not standalone_provider.has_data( chrom ): - return messages.NO_DATA - #valid_chroms = standalone_provider.valid_chroms() + 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": valid_chroms } + return { "status": messages.DATA, "valid_chroms": None } def _search_features( self, trans, dataset, query ): """ @@ -151,45 +137,32 @@ data_provider_registry = trans.app.data_provider_registry if mode == "Coverage": # Get summary using minimal cutoffs. - tracks_dataset_type = data_sources['index']['name'] - converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) - indexer = data_provider_registry.get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) + indexer = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' ) summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], detail_cutoff=0, draw_cutoff=0 ) if summary == "detail": # Use maximum level of detail--2--to get summary data no matter the resolution. summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 ) frequencies, max_v, avg_v, delta = summary - return { 'dataset_type': tracks_dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } + return { 'dataset_type': indexer.data_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto": # Only check for summary_tree if it's Auto mode (which is the default) # # Have to choose between indexer and data provider - tracks_dataset_type = data_sources['index']['name'] - converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) - indexer = data_provider_registry.get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) + indexer = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' ) summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ] ) if summary is None: - return { 'dataset_type': tracks_dataset_type, 'data': None } + return { 'dataset_type': indexer.data_type, 'data': None } if summary == "draw": kwargs["no_detail"] = True # meh extra_info = "no_detail" elif summary != "detail": frequencies, max_v, avg_v, delta = summary - return { 'dataset_type': tracks_dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } + return { 'dataset_type': indexer.data_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } # Get data provider. - if "data_standalone" in data_sources: - tracks_dataset_type = data_sources['data_standalone']['name'] - data_provider_class = data_provider_registry.get_data_provider( name=tracks_dataset_type, original_dataset=dataset ) - data_provider = data_provider_class( original_dataset=dataset ) - else: - tracks_dataset_type = data_sources['data']['name'] - data_provider_class = data_provider_registry.get_data_provider( name=tracks_dataset_type, original_dataset=dataset ) - converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) - deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type ) - data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps ) + data_provider = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='data' ) # Allow max_vals top be data provider set if not passed if max_vals is None: @@ -197,7 +170,7 @@ # Get and return data from data_provider. result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), **kwargs ) - result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } ) + result.update( { 'dataset_type': data_provider.data_type, 'extra_info': extra_info } ) return result def _raw_data( self, trans, dataset, **kwargs ): @@ -214,7 +187,7 @@ # Return data. data = None - data_provider = trans.app.data_provider_registry.get_data_provider( raw=True, original_dataset=dataset ) + data_provider = trans.app.data_provider_registry.get_data_provider( trans, raw=True, original_dataset=dataset ) if data_provider == ColumnDataProvider: #pre: should have column kwargs @@ -222,13 +195,13 @@ #TODO??: could default to first two here assert 'cols' in kwargs, ( "ColumnDataProvider needs a 'cols' parameter in the query string" ) - data = data_provider( original_dataset=dataset ).get_data( **kwargs ) + 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( original_dataset=dataset ).get_data( start=low, end=high, **kwargs ) + data = data_provider.get_data( start=low, end=high, **kwargs ) data[ 'dataset_type' ] = 'interval_index' data[ 'extra_info' ] = None if isinstance( dataset.datatype, Vcf ): diff -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 -r bdd35af2a18afde11396fcf919b5fb4cacc986ff lib/galaxy/web/api/tools.py --- a/lib/galaxy/web/api/tools.py +++ b/lib/galaxy/web/api/tools.py @@ -204,15 +204,12 @@ if run_on_regions: for jida in original_job.input_datasets: input_dataset = jida.dataset - if data_provider_registry.get_data_provider( original_dataset=input_dataset ): - # Can index dataset. - track_type, data_sources = input_dataset.datatype.get_track_type() - # Convert to datasource that provides 'data' because we need to - # extract the original data. - data_source = data_sources[ 'data' ] - msg = self.convert_dataset( trans, input_dataset, data_source ) - if msg is not None: - messages_list.append( msg ) + data_provider = data_provider_registry.get_data_provider( trans, original_dataset=input_dataset, source='data' ) + if data_provider: + if not data_provider.converted_dataset: + msg = self.convert_dataset( trans, input_dataset, data_source ) + if msg is not None: + messages_list.append( msg ) # Return any messages generated during conversions. return_message = get_highest_priority_msg( messages_list ) @@ -326,10 +323,7 @@ trans.app.security_agent.set_all_dataset_permissions( new_dataset.dataset, hda_permissions ) # Write subset of data to new dataset - data_provider_class = data_provider_registry.get_data_provider( original_dataset=input_dataset ) - data_provider = data_provider_class( original_dataset=input_dataset, - converted_dataset=converted_dataset, - dependencies=deps ) + data_provider = data_provider_registry.get_data_provider( trans, original_dataset=input_dataset, source='data' ) trans.app.object_store.create( new_dataset.dataset ) data_provider.write_data_to_file( regions, new_dataset.file_name ) diff -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 -r bdd35af2a18afde11396fcf919b5fb4cacc986ff lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -460,8 +460,9 @@ prefs = {} track_type, _ = dataset.datatype.get_track_type() - track_data_provider_class = trans.app.data_provider_registry.get_data_provider( original_dataset=dataset ) - track_data_provider = track_data_provider_class( original_dataset=dataset ) + track_data_provider = trans.app.data_provider_registry.get_data_provider( trans, + original_dataset=dataset, + source='data' ) return { "track_type": track_type, @@ -536,8 +537,8 @@ """ # Get data provider. track_type, _ = dataset.datatype.get_track_type() - track_data_provider_class = trans.app.data_provider_registry.get_data_provider( original_dataset=dataset ) - track_data_provider = track_data_provider_class( original_dataset=dataset ) + track_data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset ) + if isinstance( dataset, trans.app.model.HistoryDatasetAssociation ): hda_ldda = "hda" diff -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 -r bdd35af2a18afde11396fcf919b5fb4cacc986ff static/scripts/viz/trackster/filters.js --- a/static/scripts/viz/trackster/filters.js +++ b/static/scripts/viz/trackster/filters.js @@ -617,7 +617,8 @@ }); return { - FiltersManager: FiltersManager + FiltersManager: FiltersManager, + NumberFilter: NumberFilter }; }); diff -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 -r bdd35af2a18afde11396fcf919b5fb4cacc986ff static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,7 +1,7 @@ define( ["libs/underscore", "viz/visualization", "viz/trackster/util", "viz/trackster/slotting", "viz/trackster/painters", "mvc/data", "viz/trackster/filters" ], - function( _, visualization, util, slotting, painters, data, filters ) { + function( _, visualization, util, slotting, painters, data, filters_mod ) { var extend = _.extend; var get_random_color = util.get_random_color; @@ -587,7 +587,7 @@ moveable(this.container_div, this.drag_handle_class, ".group", this); // Set up filters. - this.filters_manager = new filters.FiltersManager(this); + this.filters_manager = new filters_mod.FiltersManager(this); this.header_div.after(this.filters_manager.parent_div); // For saving drawables' filter managers when group-level filtering is done: this.saved_filters_managers = []; @@ -601,7 +601,7 @@ if ('filters' in obj_dict) { // FIXME: Pass collection_dict to DrawableCollection/Drawable will make this easier. var old_manager = this.filters_manager; - this.filters_manager = new filters.FiltersManager(this, obj_dict.filters); + this.filters_manager = new filters_mod.FiltersManager(this, obj_dict.filters); old_manager.parent_div.replaceWith(this.filters_manager.parent_div); if (obj_dict.filters.visible) { @@ -761,7 +761,7 @@ if (filters.length === num_feature_tracks) { // Add new filter. // FIXME: can filter.copy() be used? - new_filter = new NumberFilter( { + new_filter = new filters_mod.NumberFilter( { name: filters[0].name, index: filters[0].index } ); @@ -2612,7 +2612,7 @@ moveable(track.container_div, track.drag_handle_class, ".group", track); // Attribute init. - this.filters_manager = new filters.FiltersManager(this, ('filters' in obj_dict ? obj_dict.filters : null)); + this.filters_manager = new filters_mod.FiltersManager(this, ('filters' in obj_dict ? obj_dict.filters : null)); // HACK: set filters manager for data manager. // FIXME: prolly need function to set filters and update data_manager reference. this.data_manager.set('filters_manager', this.filters_manager); @@ -4188,7 +4188,6 @@ } }; -// Exports return { View: View, DrawableGroup: DrawableGroup, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Push data sources/converter methods from controller mixin to dataset object.
by Bitbucket 21 Sep '12

21 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8a8dcc0d3668/ changeset: 8a8dcc0d3668 user: jgoecks date: 2012-09-21 17:52:47 summary: Push data sources/converter methods from controller mixin to dataset object. affected #: 4 files diff -r c56a600064a4add89de1c970e99983ae438b8db2 -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1248,6 +1248,56 @@ def get_visualizations( self ): return self.datatype.get_visualizations( self ) + def get_datasources( self, trans ): + """ + Returns datasources for dataset; if datasources are not available + due to indexing, indexing is started. Return value is a dictionary + with entries of type + (<datasource_type> : {<datasource_name>, <indexing_message>}). + """ + track_type, data_sources = self.datatype.get_track_type() + data_sources_dict = {} + msg = None + for source_type, data_source in data_sources.iteritems(): + if source_type == "data_standalone": + # Nothing to do. + msg = None + else: + # Convert. + msg = self.convert_dataset( trans, data_source ) + + # Store msg. + data_sources_dict[ source_type ] = { "name" : data_source, "message": msg } + + return data_sources_dict + + def convert_dataset( self, trans, target_type ): + """ + Converts a dataset to the target_type and returns a message indicating + status of the conversion. None is returned to indicate that dataset + was converted successfully. + """ + + # Get converted dataset; this will start the conversion if necessary. + try: + converted_dataset = self.get_converted_dataset( trans, target_type ) + except NoConverterException: + return messages.NO_CONVERTER + except ConverterDependencyException, dep_error: + return { 'kind': messages.ERROR, 'message': dep_error.value } + + # Check dataset state and return any messages. + msg = None + if converted_dataset and converted_dataset.state == trans.app.model.Dataset.states.ERROR: + job_id = trans.sa_session.query( trans.app.model.JobToOutputDatasetAssociation ) \ + .filter_by( dataset_id=converted_dataset.id ).first().job_id + job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) + msg = { 'kind': messages.ERROR, 'message': job.stderr } + elif not converted_dataset or converted_dataset.state != trans.app.model.Dataset.states.OK: + msg = messages.PENDING + + return msg + class HistoryDatasetAssociation( DatasetInstance ): def __init__( self, hid = None, diff -r c56a600064a4add89de1c970e99983ae438b8db2 -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -80,7 +80,7 @@ return msg # Get datasources and check for messages. - data_sources = self._get_datasources( trans, dataset ) + data_sources = dataset.get_datasources( trans ) messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] msg = get_highest_priority_msg( messages_list ) if msg: @@ -139,7 +139,7 @@ return msg # Get datasources and check for messages. - data_sources = self._get_datasources( trans, dataset ) + data_sources = dataset.get_datasources( trans ) messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] return_message = get_highest_priority_msg( messages_list ) if return_message: diff -r c56a600064a4add89de1c970e99983ae438b8db2 -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -312,33 +312,6 @@ if dataset.state != trans.app.model.Job.states.OK: return messages.PENDING return None - - def convert_dataset( self, trans, dataset, target_type ): - """ - Converts a dataset to the target_type and returns a message indicating - status of the conversion. None is returned to indicate that dataset - was converted successfully. - """ - - # Get converted dataset; this will start the conversion if necessary. - try: - converted_dataset = dataset.get_converted_dataset( trans, target_type ) - except NoConverterException: - return messages.NO_CONVERTER - except ConverterDependencyException, dep_error: - return { 'kind': messages.ERROR, 'message': dep_error.value } - - # Check dataset state and return any messages. - msg = None - if converted_dataset and converted_dataset.state == trans.app.model.Dataset.states.ERROR: - job_id = trans.sa_session.query( trans.app.model.JobToOutputDatasetAssociation ) \ - .filter_by( dataset_id=converted_dataset.id ).first().job_id - job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) - msg = { 'kind': messages.ERROR, 'message': job.stderr } - elif not converted_dataset or converted_dataset.state != trans.app.model.Dataset.states.OK: - msg = messages.PENDING - - return msg class UsesLibraryMixin: @@ -625,29 +598,6 @@ return visualization - def _get_datasources( self, trans, dataset ): - """ - Returns datasources for dataset; if datasources are not available - due to indexing, indexing is started. Return value is a dictionary - with entries of type - (<datasource_type> : {<datasource_name>, <indexing_message>}). - """ - track_type, data_sources = dataset.datatype.get_track_type() - data_sources_dict = {} - msg = None - for source_type, data_source in data_sources.iteritems(): - if source_type == "data_standalone": - # Nothing to do. - msg = None - else: - # Convert. - msg = self.convert_dataset( trans, dataset, data_source ) - - # Store msg. - data_sources_dict[ source_type ] = { "name" : data_source, "message": msg } - - return data_sources_dict - class UsesStoredWorkflowMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use StoredWorkflow objects. """ def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): diff -r c56a600064a4add89de1c970e99983ae438b8db2 -r 8a8dcc0d36687fcfaaa1ae26e136e76b4a0d7bb0 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -755,7 +755,7 @@ for track in tracks: # Get dataset and indexed datatype. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) - data_sources = self._get_datasources( trans, dataset ) + data_sources = dataset.get_datasources( trans ) data_provider_registry = trans.app.data_provider_registry if 'data_standalone' in data_sources: indexed_type = data_sources['data_standalone']['name'] 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: Add the ability to review tools migration stages that are available for the current Galaxy instance.
by Bitbucket 21 Sep '12

21 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c56a600064a4/ changeset: c56a600064a4 user: greg date: 2012-09-21 17:21:38 summary: Add the ability to review tools migration stages that are available for the current Galaxy instance. affected #: 4 files diff -r cd739bd3dca4859fecfe499fc976b0e0b6478238 -r c56a600064a4add89de1c970e99983ae438b8db2 lib/galaxy/tool_shed/migrate/versions/0004_tools.py --- a/lib/galaxy/tool_shed/migrate/versions/0004_tools.py +++ b/lib/galaxy/tool_shed/migrate/versions/0004_tools.py @@ -1,9 +1,9 @@ """ The NCBI BLAST+ tools have been eliminated from the distribution. The tools and -datatypes are are now available in repositories named ncbi_blast_plus and -blast_datatypes, respectively, from the main Galaxy tool shed at -http://toolshed.g2.bx.psu.edu will be installed into your local Galaxy instance -at the location discussed above by running the following command. +datatypes are now available in repositories named ncbi_blast_plus and +blast_datatypes, in the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu. +These repositories will be installed into your local Galaxy instance at the +location discussed above by running the following command. """ import sys diff -r cd739bd3dca4859fecfe499fc976b0e0b6478238 -r c56a600064a4add89de1c970e99983ae438b8db2 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -8,8 +8,10 @@ from galaxy.actions.admin import AdminActions from galaxy.web.params import QuotaParamParser from galaxy.exceptions import * +from galaxy.util.odict import * +from galaxy.tool_shed.encoding_util import * import galaxy.datatypes.registry -import logging +import logging, imp, subprocess, urllib2 log = logging.getLogger( __name__ ) @@ -685,6 +687,75 @@ if emails is None: emails = [ u.email for u in trans.sa_session.query( trans.app.model.User ).enable_eagerloads( False ).all() ] return trans.fill_template( 'admin/impersonate.mako', emails=emails, message=message, status=status ) + def get_tool_shed_url_from_tools_xml_file_path( self, trans, tool_shed ): + search_str = '://%s' % tool_shed + for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): + if shed_url.find( search_str ) >= 0: + if shed_url.endswith( '/' ): + shed_url = shed_url.rstrip( '/' ) + return shed_url + return None + def check_for_tool_dependencies( self, trans, migration_stage ): + # Get the 000x_tools.xml file associated with migration_stage. + tools_xml_file_path = os.path.abspath( os.path.join( trans.app.config.root, 'scripts', 'migrate_tools', '%04d_tools.xml' % migration_stage ) ) + tree = util.parse_xml( tools_xml_file_path ) + root = tree.getroot() + tool_shed = root.get( 'name' ) + tool_shed_url = self.get_tool_shed_url_from_tools_xml_file_path( trans, tool_shed ) + repo_name_dependency_tups = [] + if tool_shed_url: + for elem in root: + if elem.tag == 'repository': + tool_dependencies = [] + 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' % \ + ( tool_shed_url, repository_name, changeset_revision ) + response = urllib2.urlopen( url ) + text = response.read() + response.close() + if text: + tool_dependencies_dict = tool_shed_decode( text ) + for dependency_key, requirements_dict in tool_dependencies_dict.items(): + tool_dependency_name = requirements_dict[ 'name' ] + tool_dependency_version = requirements_dict[ 'version' ] + tool_dependency_type = requirements_dict[ 'type' ] + tool_dependency_readme = requirements_dict.get( 'readme', '' ) + tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) ) + repo_name_dependency_tups.append( ( repository_name, tool_dependencies ) ) + return repo_name_dependency_tups + @web.expose + @web.require_admin + def review_tool_migration_stages( self, trans, **kwd ): + message = util.restore_text( kwd.get( 'message', '' ) ) + status = util.restore_text( kwd.get( 'status', 'done' ) ) + migration_stages_dict = odict() + migration_modules = [] + migration_scripts_dir = os.path.abspath( os.path.join( trans.app.config.root, 'lib', 'galaxy', 'tool_shed', 'migrate', 'versions' ) ) + migration_scripts_dir_contents = os.listdir( migration_scripts_dir ) + for item in migration_scripts_dir_contents: + if os.path.isfile( os.path.join( migration_scripts_dir, item ) ) and item.endswith( '.py' ): + module = item.replace( '.py', '' ) + migration_modules.append( module ) + if migration_modules: + migration_modules.sort() + # Remove the 0001_tools.py script since it is the seed. + migration_modules = migration_modules[ 1: ] + # Reverse the list so viewing will be newest to oldest. + migration_modules.reverse() + for migration_module in migration_modules: + migration_stage = int( migration_module.replace( '_tools', '' ) ) + repo_name_dependency_tups = self.check_for_tool_dependencies( trans, migration_stage ) + open_file_obj, file_name, description = imp.find_module( migration_module, [ migration_scripts_dir ] ) + imported_module = imp.load_module( 'upgrade', open_file_obj, file_name, description ) + migration_info = imported_module.__doc__ + open_file_obj.close() + migration_stages_dict[ migration_stage ] = ( migration_info, repo_name_dependency_tups ) + return trans.fill_template( 'admin/review_tool_migration_stages.mako', + migration_stages_dict=migration_stages_dict, + message=message, + status=status ) @web.expose @web.require_admin def view_datatypes_registry( self, trans, **kwd ): diff -r cd739bd3dca4859fecfe499fc976b0e0b6478238 -r c56a600064a4add89de1c970e99983ae438b8db2 templates/admin/review_tool_migration_stages.mako --- /dev/null +++ b/templates/admin/review_tool_migration_stages.mako @@ -0,0 +1,120 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Tool migrations that can be performed on this Galaxy instance</div> + <div class="toolFormBody"> + <div class="form-row"> + <p> + The list of tool migration stages below, displayed most recent to oldest, provides information about the repositories in the + main Galaxy tool shed that will be cloned at each stage if you run the shell command for that stage. This enables you to execute + the migration process for any stage at any time. + </p> + <p> + Keep in mind that tools included in a repository that you want to be displayed in the Galaxy tool panel when the repository is + installed must be defined in the <b>tool_conf.xml</b> (or equivalent) config file prior to execution of the migration process for a + stage. Executing a migration process multiple times will have no affect unless the repositories associated with that stage have been + uninstalled prior to the execution of the migration process. + </p> + <p> + When you initiate a migration process, the associated repositories will be cloned from the Galaxy tool shed at + <a href="http://toolshed.g2.bx.psu.edu" target="_blank">http://toolshed.g2.bx.psu.edu</a>. The location in which the tool repositories + will be installed is the value of the 'tool_path' attribute in the <tool> tag of the file named ./migrated_tool_conf.xml + (i.e., <b><toolbox tool_path="../shed_tools"></b>). The default location setting is <b>'../shed_tools'</b>, which may be problematic + for some cluster environments, so make sure to change it before you execute the installation process if appropriate. The configured location + must be outside of the Galaxy installation directory or it must be in a sub-directory protected by a properly configured <b>.hgignore</b> + file if the directory is within the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using + mercurial's clone feature, which creates .hg directories and associated mercurial repository files. Not having <b>.hgignore</b> properly + configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed repositories if they are + in directories that pose conflicts. See mercurial's .hgignore documentation at + <a href="http://mercurial.selenic.com/wiki/.hgignore" target="_blank">http://mercurial.selenic.com/wiki/.hgignore</a> for details. + </p> + </div> + <table class="grid"> + %for stage in migration_stages_dict.keys(): + <% + migration_command = 'sh ./scripts/migrate_tools/%04d_tools.sh' % stage + install_dependencies = '%s install_dependencies' % migration_command + migration_tup = migration_stages_dict[ stage ] + migration_info, repo_name_dependency_tups = migration_tup + repository_names = [] + for repo_name_dependency_tup in repo_name_dependency_tups: + repository_name, tool_dependencies = repo_name_dependency_tup + if repository_name not in repository_names: + repository_names.append( repository_name ) + if repository_names: + repository_names.sort() + repository_names = ', '.join( repository_names ) + %> + <tr><td bgcolor="#D8D8D8"><b>Tool migration stage ${stage} - repositories: ${repository_names}</b></td></tr> + <tr> + <td bgcolor="#FFFFCC"> + <div class="form-row"> + <p>${migration_info} <b>Run commands from the Galaxy installation directory!</b></p> + <p> + %if tool_dependencies: + This migration stage includes tools that have tool dependencies that can be automatically installed. To install them, run:<br/> + <b>${install_dependencies}</b><br/><br/> + To skip tool dependency installation run:<br/> + <b>${migration_command}</b> + %else: + <b>${migration_command}</b> + %endif + </p> + </div> + </td> + </tr> + %for repo_name_dependency_tup in repo_name_dependency_tups: + <% repository_name, tool_dependencies = repo_name_dependency_tup %> + <tr> + <td bgcolor="#DADFEF"> + <div class="form-row"> + <b>Repository:</b> ${repository_name} + </div> + </td> + </tr> + %if tool_dependencies: + <tr> + <td> + <div class="form-row"> + <b>Tool dependencies</b> + </div> + </td> + </tr> + %for tool_dependencies_tup in tool_dependencies: + <% + tool_dependency_name = tool_dependencies_tup[0] + tool_dependency_version = tool_dependencies_tup[1] + tool_dependency_type = tool_dependencies_tup[2] + installation_requirements = tool_dependencies_tup[3].replace( '\n', '<br/>' ) + %> + <tr> + <td> + <div class="form-row"> + <b>Name:</b> ${tool_dependency_name} <b>Version:</b> ${tool_dependency_version} <b>Type:</b> ${tool_dependency_type} + </div> + <div class="form-row"> + <b>Requirements and installation information:</b><br/> + ${installation_requirements} + </div> + </td> + </tr> + %endfor + %else: + <tr> + <td> + <div class="form-row"> + No tool dependencies have been defined for this repository. + </div> + </td> + </tr> + %endif + %endfor + %endfor + </table> + </div> +</div> diff -r cd739bd3dca4859fecfe499fc976b0e0b6478238 -r c56a600064a4add89de1c970e99983ae438b8db2 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -66,10 +66,11 @@ <div class="toolSectionBody"><div class="toolSectionBg"><div class="toolTitle"><a href="${h.url_for( controller='admin', action='view_datatypes_registry' )}" target="galaxy_main">View datatypes registry</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='tool_versions' )}" target="galaxy_main">Tool versions</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='tool_versions' )}" target="galaxy_main">View tool lineage</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='reload_tool' )}" target="galaxy_main">Reload a tool's configuration</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='memdump' )}" target="galaxy_main">Profile memory usage</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='jobs' )}" target="galaxy_main">Manage jobs</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='review_tool_migration_stages' )}" target="galaxy_main">Review tool migration stages</a></div> %if installing_repository_ids: <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='monitor_repository_installation', tool_shed_repository_ids=installing_repository_ids )}" target="galaxy_main">Monitor installing tool shed repositories</a></div> %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Place track filters in their own file.
by Bitbucket 21 Sep '12

21 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cd739bd3dca4/ changeset: cd739bd3dca4 user: jgoecks date: 2012-09-21 17:14:56 summary: Place track filters in their own file. affected #: 2 files diff -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 -r cd739bd3dca4859fecfe499fc976b0e0b6478238 static/scripts/viz/trackster/filters.js --- /dev/null +++ b/static/scripts/viz/trackster/filters.js @@ -0,0 +1,623 @@ +define( ["libs/underscore"], function(_) { + +var extend = _.extend; + +/** + * Filters that enable users to show/hide data points dynamically. + */ +var Filter = function(obj_dict) { + this.manager = null; + this.name = obj_dict.name; + // Index into payload to filter. + this.index = obj_dict.index; + this.tool_id = obj_dict.tool_id; + // Name to use for filter when building expression for tool. + this.tool_exp_name = obj_dict.tool_exp_name; +}; + +extend(Filter.prototype, { + /** + * Convert filter to dictionary. + */ + to_dict: function() { + return { + name: this.name, + index: this.index, + tool_id: this.tool_id, + tool_exp_name: this.tool_exp_name + }; + } +}); + +/** + * Creates an action icon. + */ +var create_action_icon = function(title, css_class, on_click_fn) { + return $("<a/>").attr("href", "javascript:void(0);").attr("title", title) + .addClass("icon-button").addClass(css_class).tooltip() + .click(on_click_fn); +}; + +/** + * Number filters have a min, max as well as a low, high; low and high are used + */ +var NumberFilter = function(obj_dict) { + // + // Attribute init. + // + Filter.call(this, obj_dict); + // Filter low/high. These values are used to filter elements. + this.low = ('low' in obj_dict ? obj_dict.low : -Number.MAX_VALUE); + this.high = ('high' in obj_dict ? obj_dict.high : Number.MAX_VALUE); + // Slide min/max. These values are used to set/update slider. + this.min = ('min' in obj_dict ? obj_dict.min : Number.MAX_VALUE); + this.max = ('max' in obj_dict ? obj_dict.max : -Number.MAX_VALUE); + // UI elements associated with filter. + this.container = null; + this.slider = null; + this.slider_label = null; + + // + // Create HTML. + // + + // Function that supports inline text editing of slider values. + // Enable users to edit parameter's value via a text box. + var edit_slider_values = function(container, span, slider) { + container.click(function() { + var cur_value = span.text(), + max = parseFloat(slider.slider("option", "max")), + input_size = (max <= 1 ? 4 : max <= 1000000 ? max.toString().length : 6), + multi_value = false, + slider_row = $(this).parents(".slider-row"); + + // Row now has input. + slider_row.addClass("input"); + + // Increase input size if there are two values. + if (slider.slider("option", "values")) { + input_size = 2*input_size + 1; + multi_value = true; + } + span.text(""); + // Temporary input for changing value. + $("<input type='text'/>").attr("size", input_size).attr("maxlength", input_size) + .attr("value", cur_value).appendTo(span).focus().select() + .click(function(e) { + // Don't want click to propogate up to values_span and restart everything. + e.stopPropagation(); + }).blur(function() { + $(this).remove(); + span.text(cur_value); + slider_row.removeClass("input"); + }).keyup(function(e) { + if (e.keyCode === 27) { + // Escape key. + $(this).trigger("blur"); + } else if (e.keyCode === 13) { + // + // Enter/return key initiates callback. If new value(s) are in slider range, + // change value (which calls slider's change() function). + // + var slider_min = slider.slider("option", "min"), + slider_max = slider.slider("option", "max"), + invalid = function(a_val) { + return (isNaN(a_val) || a_val > slider_max || a_val < slider_min); + }, + new_value = $(this).val(); + if (!multi_value) { + new_value = parseFloat(new_value); + if (invalid(new_value)) { + alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]"); + return $(this); + } + } + else { // Multi value. + new_value = new_value.split("-"); + new_value = [parseFloat(new_value[0]), parseFloat(new_value[1])]; + if (invalid(new_value[0]) || invalid(new_value[1])) { + alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]"); + return $(this); + } + } + + // Updating the slider also updates slider values and removes input. + slider.slider((multi_value ? "values" : "value"), new_value); + slider_row.removeClass("input"); + } + }); + }); + }; + + var filter = this; + + filter.parent_div = $("<div/>").addClass("filter-row slider-row"); + + // Set up filter label (name, values). + var filter_label = $("<div/>").addClass("elt-label").appendTo(filter.parent_div), + name_span = $("<span/>").addClass("slider-name").text(filter.name + " ").appendTo(filter_label), + values_span = $("<span/>").text(this.low + "-" + this.high), + values_span_container = $("<span/>").addClass("slider-value").appendTo(filter_label).append("[").append(values_span).append("]"); + filter.values_span = values_span; + + // Set up slider for filter. + var slider_div = $("<div/>").addClass("slider").appendTo(filter.parent_div); + filter.control_element = $("<div/>").attr("id", filter.name + "-filter-control").appendTo(slider_div); + filter.control_element.slider({ + range: true, + min: this.min, + max: this.max, + step: this.get_slider_step(this.min, this.max), + values: [this.low, this.high], + slide: function(event, ui) { + filter.slide(event, ui); + }, + change: function(event, ui) { + filter.control_element.slider("option", "slide").call(filter.control_element, event, ui); + } + }); + filter.slider = filter.control_element; + filter.slider_label = values_span; + + // Enable users to edit slider values via text box. + edit_slider_values(values_span_container, values_span, filter.control_element); + + // Set up filter display controls. + var display_controls_div = $("<div/>").addClass("display-controls").appendTo(filter.parent_div); + this.transparency_icon = create_action_icon("Use filter for data transparency", "layer-transparent", + function() { + if (filter.manager.alpha_filter !== filter) { + // Setting this filter as the alpha filter. + filter.manager.alpha_filter = filter; + // Update UI for new filter. + filter.manager.parent_div.find(".layer-transparent").removeClass("active").hide(); + filter.transparency_icon.addClass("active").show(); + } + else { + // Clearing filter as alpha filter. + filter.manager.alpha_filter = null; + filter.transparency_icon.removeClass("active"); + } + filter.manager.track.request_draw(true, true); + } ) + .appendTo(display_controls_div).hide(); + this.height_icon = create_action_icon("Use filter for data height", "arrow-resize-090", + function() { + if (filter.manager.height_filter !== filter) { + // Setting this filter as the height filter. + filter.manager.height_filter = filter; + // Update UI for new filter. + filter.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(); + filter.height_icon.addClass("active").show(); + } + else { + // Clearing filter as alpha filter. + filter.manager.height_filter = null; + filter.height_icon.removeClass("active"); + } + filter.manager.track.request_draw(true, true); + } ) + .appendTo(display_controls_div).hide(); + filter.parent_div.hover( function() { + filter.transparency_icon.show(); + filter.height_icon.show(); + }, + function() { + if (filter.manager.alpha_filter !== filter) { + filter.transparency_icon.hide(); + } + if (filter.manager.height_filter !== filter) { + filter.height_icon.hide(); + } + } ); + + // Add to clear floating layout. + $("<div style='clear: both;'/>").appendTo(filter.parent_div); +}; +extend(NumberFilter.prototype, { + /** + * Convert filter to dictionary. + */ + to_dict: function() { + var obj_dict = Filter.prototype.to_dict.call(this); + return extend(obj_dict, { + type: 'number', + min: this.min, + max: this.max, + low: this.low, + high: this.high + }); + }, + /** + * Return a copy of filter. + */ + copy: function() { + return new NumberFilter( + { + name: this.name, + index: this.index, + tool_id: this.tool_id, + tool_exp_name: this.tool_exp_name + }); + }, + /** + * Get step for slider. + */ + // FIXME: make this a "static" function. + get_slider_step: function(min, max) { + var range = max - min; + return (range <= 2 ? 0.01 : 1); + }, + /** + * Handle slide events. + */ + slide: function(event, ui) { + var values = ui.values; + + // Set new values in UI. + this.values_span.text(values[0] + "-" + values[1]); + + // Set new values in filter. + this.low = values[0]; + this.high = values[1]; + + // Set timeout to update if filter low, high are stable. + var self = this; + setTimeout(function() { + if (values[0] === self.low && values[1] === self.high) { + self.manager.track.request_draw(true, true); + } + }, 25); + + }, + /** + * Returns true if filter can be applied to element. + */ + applies_to: function(element) { + if (element.length > this.index) { + return true; + } + return false; + }, + /** + * Helper function: returns true if value in in filter's [low, high] range. + */ + _keep_val: function(val) { + return (isNaN(val) || (val >= this.low && val <= this.high)); + }, + /** + * Returns true if (a) element's value(s) is in [low, high] (range is inclusive) + * or (b) if value is non-numeric and hence unfilterable. + */ + keep: function(element) { + if ( !this.applies_to( element ) ) { + // No element to filter on. + return true; + } + + // Keep value function. + var filter = this; + + // Do filtering. + var to_filter = element[this.index]; + if (to_filter instanceof Array) { + var returnVal = true; + for (var i = 0; i < to_filter.length; i++) { + if (!this._keep_val(to_filter[i])) { + // Exclude element. + returnVal = false; + break; + } + } + return returnVal; + } + else { + return this._keep_val(element[this.index]); + } + }, + /** + * Update filter's min and max values based on element's values. + */ + update_attrs: function(element) { + var updated = false; + if (!this.applies_to(element) ) { + return updated; + } + + // + // Update filter's min, max based on element values. + // + + // Make value(s) into an Array. + var values = element[this.index]; + if (!(values instanceof Array)) { + values = [values]; + } + + // Loop through values and update min, max. + for (var i = 0; i < values.length; i++) { + var value = values[i]; + if (value < this.min) { + this.min = Math.floor(value); + updated = true; + } + if (value > this.max) { + this.max = Math.ceil(value); + updated = true; + } + } + return updated; + }, + /** + * Update filter's slider. + */ + update_ui_elt: function () { + // Only show filter if min < max because filter is not useful otherwise. This + // covers all corner cases, such as when min, max have not been defined and + // when min == max. + if (this.min < this.max) { + this.parent_div.show(); + } + else { + this.parent_div.hide(); + } + + var + slider_min = this.slider.slider("option", "min"), + slider_max = this.slider.slider("option", "max"); + if (this.min < slider_min || this.max > slider_max) { + // Update slider min, max, step. + this.slider.slider("option", "min", this.min); + this.slider.slider("option", "max", this.max); + this.slider.slider("option", "step", this.get_slider_step(this.min, this.max)); + // Refresh slider: + // TODO: do we want to keep current values or reset to min/max? + // Currently we reset values: + this.slider.slider("option", "values", [this.min, this.max]); + // To use the current values. + //var values = this.slider.slider( "option", "values" ); + //this.slider.slider( "option", "values", values ); + } + } +}); + +/** + * Manages a set of filters. + */ +var FiltersManager = function(track, obj_dict) { + this.track = track; + this.alpha_filter = null; + this.height_filter = null; + this.filters = []; + + // + // Create HTML. + // + + // + // Create parent div. + // + this.parent_div = $("<div/>").addClass("filters").hide(); + // Disable dragging, double clicking, keys on div so that actions on slider do not impact viz. + this.parent_div.bind("drag", function(e) { + e.stopPropagation(); + }).click(function(e) { + e.stopPropagation(); + }).bind("dblclick", function(e) { + e.stopPropagation(); + }).bind("keydown", function(e) { + e.stopPropagation(); + }); + + // + // Restore state from dict. + // + if (obj_dict && 'filters' in obj_dict) { // Second condition needed for backward compatibility. + var + alpha_filter_name = ('alpha_filter' in obj_dict ? obj_dict.alpha_filter : null), + height_filter_name = ('height_filter' in obj_dict ? obj_dict.height_filter : null), + filters_dict = obj_dict.filters, + filter; + for (var i = 0; i < filters_dict.length; i++) { + if (filters_dict[i].type === 'number') { + filter = new NumberFilter(filters_dict[i]); + this.add_filter(filter); + if (filter.name === alpha_filter_name) { + this.alpha_filter = filter; + filter.transparency_icon.addClass("active").show(); + } + if (filter.name === height_filter_name) { + this.height_filter = filter; + filter.height_icon.addClass("active").show(); + } + } + else { + console.log("ERROR: unsupported filter: ", name, type); + } + } + + + if ('visible' in obj_dict && obj_dict.visible) { + this.parent_div.show(); + } + } + + // Add button to filter complete dataset. + if (this.filters.length !== 0) { + var run_buttons_row = $("<div/>").addClass("param-row").appendTo(this.parent_div); + var run_on_dataset_button = $("<input type='submit'/>").attr("value", "Run on complete dataset").appendTo(run_buttons_row); + var filter_manager = this; + run_on_dataset_button.click( function() { + filter_manager.run_on_dataset(); + }); + } + +}; + +extend(FiltersManager.prototype, { + // HTML manipulation and inspection. + show: function() { this.parent_div.show(); }, + hide: function() { this.parent_div.hide(); }, + toggle: function() { this.parent_div.toggle(); }, + visible: function() { return this.parent_div.is(":visible"); }, + /** + * Returns dictionary for manager. + */ + to_dict: function() { + var obj_dict = {}, + filter_dicts = [], + filter; + + // Include individual filter states. + for (var i = 0; i < this.filters.length; i++) { + filter = this.filters[i]; + filter_dicts.push(filter.to_dict()); + } + obj_dict.filters = filter_dicts; + + // Include transparency, height filters. + obj_dict.alpha_filter = (this.alpha_filter ? this.alpha_filter.name : null); + obj_dict.height_filter = (this.height_filter ? this.height_filter.name : null); + + // Include visibility. + obj_dict.visible = this.parent_div.is(":visible"); + + return obj_dict; + }, + /** + * Return a copy of the manager. + */ + copy: function(new_track) { + var copy = new FiltersManager(new_track); + for (var i = 0; i < this.filters.length; i++) { + copy.add_filter(this.filters[i].copy()); + } + return copy; + }, + /** + * Add a filter to the manager. + */ + add_filter: function(filter) { + filter.manager = this; + this.parent_div.append(filter.parent_div); + this.filters.push(filter); + }, + /** + * Remove all filters from manager. + */ + remove_all: function() { + this.filters = []; + this.parent_div.children().remove(); + }, + /** + * Initialize filters. + */ + init_filters: function() { + for (var i = 0; i < this.filters.length; i++) { + var filter = this.filters[i]; + filter.update_ui_elt(); + } + }, + /** + * Clear filters so that they do not impact track display. + */ + clear_filters: function() { + for (var i = 0; i < this.filters.length; i++) { + var filter = this.filters[i]; + filter.slider.slider("option", "values", [filter.min, filter.max]); + } + this.alpha_filter = null; + this.height_filter = null; + + // Hide icons for setting filters. + this.parent_div.find(".icon-button").hide(); + }, + run_on_dataset: function() { + // Get or create dictionary item. + var get_or_create_dict_item = function(dict, key, new_item) { + // Add new item to dict if + if (!(key in dict)) { + dict[key] = new_item; + } + return dict[key]; + }; + + // + // Find and group active filters. Active filters are those being used to hide data. + // Filters with the same tool id are grouped. + // + var active_filters = {}, + filter, + tool_filter_conditions; + for (var i = 0; i < this.filters.length; i++) { + filter = this.filters[i]; + if (filter.tool_id) { + // Add filtering conditions if filter low/high are set. + if (filter.min !== filter.low) { + tool_filter_conditions = get_or_create_dict_item(active_filters, filter.tool_id, []); + tool_filter_conditions[tool_filter_conditions.length] = filter.tool_exp_name + " >= " + filter.low; + } + if (filter.max !== filter.high) { + tool_filter_conditions = get_or_create_dict_item(active_filters, filter.tool_id, []); + tool_filter_conditions[tool_filter_conditions.length] = filter.tool_exp_name + " <= " + filter.high; + } + } + } + + // + // Use tools to run filters. + // + + // Create list of (tool_id, tool_filters) tuples. + var active_filters_list = []; + for (var tool_id in active_filters) { + active_filters_list[active_filters_list.length] = [tool_id, active_filters[tool_id]]; + } + + // Invoke recursive function to run filters; this enables chaining of filters via + // iteratively application. + (function run_filter(input_dataset_id, filters) { + var + // Set up filtering info and params. + filter_tuple = filters[0], + tool_id = filter_tuple[0], + tool_filters = filter_tuple[1], + tool_filter_str = "(" + tool_filters.join(") and (") + ")", + url_params = { + cond: tool_filter_str, + input: input_dataset_id, + target_dataset_id: input_dataset_id, + tool_id: tool_id + }; + + // Remove current filter. + filters = filters.slice(1); + + $.getJSON(run_tool_url, url_params, function(response) { + if (response.error) { + // General error. + show_modal("Filter Dataset", + "Error running tool " + tool_id, + { "Close" : hide_modal } ); + } + else if (filters.length === 0) { + // No more filters to run. + show_modal("Filtering Dataset", + "Filter(s) are running on the complete dataset. Outputs are in dataset's history.", + { "Close" : hide_modal } ); + } + else { + // More filters to run. + run_filter(response.dataset_id, filters); + } + }); + + })(this.track.dataset_id, active_filters_list); + } +}); + +return { + FiltersManager: FiltersManager +}; + +}); diff -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 -r cd739bd3dca4859fecfe499fc976b0e0b6478238 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,6 +1,7 @@ define( ["libs/underscore", "viz/visualization", "viz/trackster/util", - "viz/trackster/slotting", "viz/trackster/painters", "mvc/data" ], - function( _, visualization, util, slotting, painters, data ) { + "viz/trackster/slotting", "viz/trackster/painters", "mvc/data", + "viz/trackster/filters" ], + function( _, visualization, util, slotting, painters, data, filters ) { var extend = _.extend; var get_random_color = util.get_random_color; @@ -586,7 +587,7 @@ moveable(this.container_div, this.drag_handle_class, ".group", this); // Set up filters. - this.filters_manager = new FiltersManager(this); + this.filters_manager = new filters.FiltersManager(this); this.header_div.after(this.filters_manager.parent_div); // For saving drawables' filter managers when group-level filtering is done: this.saved_filters_managers = []; @@ -600,7 +601,7 @@ if ('filters' in obj_dict) { // FIXME: Pass collection_dict to DrawableCollection/Drawable will make this easier. var old_manager = this.filters_manager; - this.filters_manager = new FiltersManager(this, obj_dict.filters); + this.filters_manager = new filters.FiltersManager(this, obj_dict.filters); old_manager.parent_div.replaceWith(this.filters_manager.parent_div); if (obj_dict.filters.visible) { @@ -1831,619 +1832,6 @@ }); /** - * Filters that enable users to show/hide data points dynamically. - */ -var Filter = function(obj_dict) { - this.manager = null; - this.name = obj_dict.name; - // Index into payload to filter. - this.index = obj_dict.index; - this.tool_id = obj_dict.tool_id; - // Name to use for filter when building expression for tool. - this.tool_exp_name = obj_dict.tool_exp_name; -}; - -extend(Filter.prototype, { - /** - * Convert filter to dictionary. - */ - to_dict: function() { - return { - name: this.name, - index: this.index, - tool_id: this.tool_id, - tool_exp_name: this.tool_exp_name - }; - } -}); - -/** - * Creates an action icon. - */ -var create_action_icon = function(title, css_class, on_click_fn) { - return $("<a/>").attr("href", "javascript:void(0);").attr("title", title) - .addClass("icon-button").addClass(css_class).tooltip() - .click(on_click_fn); -}; - -/** - * Number filters have a min, max as well as a low, high; low and high are used - */ -var NumberFilter = function(obj_dict) { - // - // Attribute init. - // - Filter.call(this, obj_dict); - // Filter low/high. These values are used to filter elements. - this.low = ('low' in obj_dict ? obj_dict.low : -Number.MAX_VALUE); - this.high = ('high' in obj_dict ? obj_dict.high : Number.MAX_VALUE); - // Slide min/max. These values are used to set/update slider. - this.min = ('min' in obj_dict ? obj_dict.min : Number.MAX_VALUE); - this.max = ('max' in obj_dict ? obj_dict.max : -Number.MAX_VALUE); - // UI elements associated with filter. - this.container = null; - this.slider = null; - this.slider_label = null; - - // - // Create HTML. - // - - // Function that supports inline text editing of slider values. - // Enable users to edit parameter's value via a text box. - var edit_slider_values = function(container, span, slider) { - container.click(function() { - var cur_value = span.text(), - max = parseFloat(slider.slider("option", "max")), - input_size = (max <= 1 ? 4 : max <= 1000000 ? max.toString().length : 6), - multi_value = false, - slider_row = $(this).parents(".slider-row"); - - // Row now has input. - slider_row.addClass("input"); - - // Increase input size if there are two values. - if (slider.slider("option", "values")) { - input_size = 2*input_size + 1; - multi_value = true; - } - span.text(""); - // Temporary input for changing value. - $("<input type='text'/>").attr("size", input_size).attr("maxlength", input_size) - .attr("value", cur_value).appendTo(span).focus().select() - .click(function(e) { - // Don't want click to propogate up to values_span and restart everything. - e.stopPropagation(); - }).blur(function() { - $(this).remove(); - span.text(cur_value); - slider_row.removeClass("input"); - }).keyup(function(e) { - if (e.keyCode === 27) { - // Escape key. - $(this).trigger("blur"); - } else if (e.keyCode === 13) { - // - // Enter/return key initiates callback. If new value(s) are in slider range, - // change value (which calls slider's change() function). - // - var slider_min = slider.slider("option", "min"), - slider_max = slider.slider("option", "max"), - invalid = function(a_val) { - return (isNaN(a_val) || a_val > slider_max || a_val < slider_min); - }, - new_value = $(this).val(); - if (!multi_value) { - new_value = parseFloat(new_value); - if (invalid(new_value)) { - alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]"); - return $(this); - } - } - else { // Multi value. - new_value = new_value.split("-"); - new_value = [parseFloat(new_value[0]), parseFloat(new_value[1])]; - if (invalid(new_value[0]) || invalid(new_value[1])) { - alert("Parameter value must be in the range [" + slider_min + "-" + slider_max + "]"); - return $(this); - } - } - - // Updating the slider also updates slider values and removes input. - slider.slider((multi_value ? "values" : "value"), new_value); - slider_row.removeClass("input"); - } - }); - }); - }; - - var filter = this; - - filter.parent_div = $("<div/>").addClass("filter-row slider-row"); - - // Set up filter label (name, values). - var filter_label = $("<div/>").addClass("elt-label").appendTo(filter.parent_div), - name_span = $("<span/>").addClass("slider-name").text(filter.name + " ").appendTo(filter_label), - values_span = $("<span/>").text(this.low + "-" + this.high), - values_span_container = $("<span/>").addClass("slider-value").appendTo(filter_label).append("[").append(values_span).append("]"); - filter.values_span = values_span; - - // Set up slider for filter. - var slider_div = $("<div/>").addClass("slider").appendTo(filter.parent_div); - filter.control_element = $("<div/>").attr("id", filter.name + "-filter-control").appendTo(slider_div); - filter.control_element.slider({ - range: true, - min: this.min, - max: this.max, - step: this.get_slider_step(this.min, this.max), - values: [this.low, this.high], - slide: function(event, ui) { - filter.slide(event, ui); - }, - change: function(event, ui) { - filter.control_element.slider("option", "slide").call(filter.control_element, event, ui); - } - }); - filter.slider = filter.control_element; - filter.slider_label = values_span; - - // Enable users to edit slider values via text box. - edit_slider_values(values_span_container, values_span, filter.control_element); - - // Set up filter display controls. - var display_controls_div = $("<div/>").addClass("display-controls").appendTo(filter.parent_div); - this.transparency_icon = create_action_icon("Use filter for data transparency", "layer-transparent", - function() { - if (filter.manager.alpha_filter !== filter) { - // Setting this filter as the alpha filter. - filter.manager.alpha_filter = filter; - // Update UI for new filter. - filter.manager.parent_div.find(".layer-transparent").removeClass("active").hide(); - filter.transparency_icon.addClass("active").show(); - } - else { - // Clearing filter as alpha filter. - filter.manager.alpha_filter = null; - filter.transparency_icon.removeClass("active"); - } - filter.manager.track.request_draw(true, true); - } ) - .appendTo(display_controls_div).hide(); - this.height_icon = create_action_icon("Use filter for data height", "arrow-resize-090", - function() { - if (filter.manager.height_filter !== filter) { - // Setting this filter as the height filter. - filter.manager.height_filter = filter; - // Update UI for new filter. - filter.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(); - filter.height_icon.addClass("active").show(); - } - else { - // Clearing filter as alpha filter. - filter.manager.height_filter = null; - filter.height_icon.removeClass("active"); - } - filter.manager.track.request_draw(true, true); - } ) - .appendTo(display_controls_div).hide(); - filter.parent_div.hover( function() { - filter.transparency_icon.show(); - filter.height_icon.show(); - }, - function() { - if (filter.manager.alpha_filter !== filter) { - filter.transparency_icon.hide(); - } - if (filter.manager.height_filter !== filter) { - filter.height_icon.hide(); - } - } ); - - // Add to clear floating layout. - $("<div style='clear: both;'/>").appendTo(filter.parent_div); -}; -extend(NumberFilter.prototype, { - /** - * Convert filter to dictionary. - */ - to_dict: function() { - var obj_dict = Filter.prototype.to_dict.call(this); - return extend(obj_dict, { - type: 'number', - min: this.min, - max: this.max, - low: this.low, - high: this.high - }); - }, - /** - * Return a copy of filter. - */ - copy: function() { - return new NumberFilter( - { - name: this.name, - index: this.index, - tool_id: this.tool_id, - tool_exp_name: this.tool_exp_name - }); - }, - /** - * Get step for slider. - */ - // FIXME: make this a "static" function. - get_slider_step: function(min, max) { - var range = max - min; - return (range <= 2 ? 0.01 : 1); - }, - /** - * Handle slide events. - */ - slide: function(event, ui) { - var values = ui.values; - - // Set new values in UI. - this.values_span.text(values[0] + "-" + values[1]); - - // Set new values in filter. - this.low = values[0]; - this.high = values[1]; - - // Set timeout to update if filter low, high are stable. - var self = this; - setTimeout(function() { - if (values[0] === self.low && values[1] === self.high) { - self.manager.track.request_draw(true, true); - } - }, 25); - - }, - /** - * Returns true if filter can be applied to element. - */ - applies_to: function(element) { - if (element.length > this.index) { - return true; - } - return false; - }, - /** - * Helper function: returns true if value in in filter's [low, high] range. - */ - _keep_val: function(val) { - return (isNaN(val) || (val >= this.low && val <= this.high)); - }, - /** - * Returns true if (a) element's value(s) is in [low, high] (range is inclusive) - * or (b) if value is non-numeric and hence unfilterable. - */ - keep: function(element) { - if ( !this.applies_to( element ) ) { - // No element to filter on. - return true; - } - - // Keep value function. - var filter = this; - - // Do filtering. - var to_filter = element[this.index]; - if (to_filter instanceof Array) { - var returnVal = true; - for (var i = 0; i < to_filter.length; i++) { - if (!this._keep_val(to_filter[i])) { - // Exclude element. - returnVal = false; - break; - } - } - return returnVal; - } - else { - return this._keep_val(element[this.index]); - } - }, - /** - * Update filter's min and max values based on element's values. - */ - update_attrs: function(element) { - var updated = false; - if (!this.applies_to(element) ) { - return updated; - } - - // - // Update filter's min, max based on element values. - // - - // Make value(s) into an Array. - var values = element[this.index]; - if (!(values instanceof Array)) { - values = [values]; - } - - // Loop through values and update min, max. - for (var i = 0; i < values.length; i++) { - var value = values[i]; - if (value < this.min) { - this.min = Math.floor(value); - updated = true; - } - if (value > this.max) { - this.max = Math.ceil(value); - updated = true; - } - } - return updated; - }, - /** - * Update filter's slider. - */ - update_ui_elt: function () { - // Only show filter if min < max because filter is not useful otherwise. This - // covers all corner cases, such as when min, max have not been defined and - // when min == max. - if (this.min < this.max) { - this.parent_div.show(); - } - else { - this.parent_div.hide(); - } - - var - slider_min = this.slider.slider("option", "min"), - slider_max = this.slider.slider("option", "max"); - if (this.min < slider_min || this.max > slider_max) { - // Update slider min, max, step. - this.slider.slider("option", "min", this.min); - this.slider.slider("option", "max", this.max); - this.slider.slider("option", "step", this.get_slider_step(this.min, this.max)); - // Refresh slider: - // TODO: do we want to keep current values or reset to min/max? - // Currently we reset values: - this.slider.slider("option", "values", [this.min, this.max]); - // To use the current values. - //var values = this.slider.slider( "option", "values" ); - //this.slider.slider( "option", "values", values ); - } - } -}); - -/** - * Manages a set of filters. - */ -var FiltersManager = function(track, obj_dict) { - this.track = track; - this.alpha_filter = null; - this.height_filter = null; - this.filters = []; - - // - // Create HTML. - // - - // - // Create parent div. - // - this.parent_div = $("<div/>").addClass("filters").hide(); - // Disable dragging, double clicking, keys on div so that actions on slider do not impact viz. - this.parent_div.bind("drag", function(e) { - e.stopPropagation(); - }).click(function(e) { - e.stopPropagation(); - }).bind("dblclick", function(e) { - e.stopPropagation(); - }).bind("keydown", function(e) { - e.stopPropagation(); - }); - - // - // Restore state from dict. - // - if (obj_dict && 'filters' in obj_dict) { // Second condition needed for backward compatibility. - var - alpha_filter_name = ('alpha_filter' in obj_dict ? obj_dict.alpha_filter : null), - height_filter_name = ('height_filter' in obj_dict ? obj_dict.height_filter : null), - filters_dict = obj_dict.filters, - filter; - for (var i = 0; i < filters_dict.length; i++) { - if (filters_dict[i].type === 'number') { - filter = new NumberFilter(filters_dict[i]); - this.add_filter(filter); - if (filter.name === alpha_filter_name) { - this.alpha_filter = filter; - filter.transparency_icon.addClass("active").show(); - } - if (filter.name === height_filter_name) { - this.height_filter = filter; - filter.height_icon.addClass("active").show(); - } - } - else { - console.log("ERROR: unsupported filter: ", name, type); - } - } - - - if ('visible' in obj_dict && obj_dict.visible) { - this.parent_div.show(); - } - } - - // Add button to filter complete dataset. - if (this.filters.length !== 0) { - var run_buttons_row = $("<div/>").addClass("param-row").appendTo(this.parent_div); - var run_on_dataset_button = $("<input type='submit'/>").attr("value", "Run on complete dataset").appendTo(run_buttons_row); - var filter_manager = this; - run_on_dataset_button.click( function() { - filter_manager.run_on_dataset(); - }); - } - -}; - -extend(FiltersManager.prototype, { - // HTML manipulation and inspection. - show: function() { this.parent_div.show(); }, - hide: function() { this.parent_div.hide(); }, - toggle: function() { this.parent_div.toggle(); }, - visible: function() { return this.parent_div.is(":visible"); }, - /** - * Returns dictionary for manager. - */ - to_dict: function() { - var obj_dict = {}, - filter_dicts = [], - filter; - - // Include individual filter states. - for (var i = 0; i < this.filters.length; i++) { - filter = this.filters[i]; - filter_dicts.push(filter.to_dict()); - } - obj_dict.filters = filter_dicts; - - // Include transparency, height filters. - obj_dict.alpha_filter = (this.alpha_filter ? this.alpha_filter.name : null); - obj_dict.height_filter = (this.height_filter ? this.height_filter.name : null); - - // Include visibility. - obj_dict.visible = this.parent_div.is(":visible"); - - return obj_dict; - }, - /** - * Return a copy of the manager. - */ - copy: function(new_track) { - var copy = new FiltersManager(new_track); - for (var i = 0; i < this.filters.length; i++) { - copy.add_filter(this.filters[i].copy()); - } - return copy; - }, - /** - * Add a filter to the manager. - */ - add_filter: function(filter) { - filter.manager = this; - this.parent_div.append(filter.parent_div); - this.filters.push(filter); - }, - /** - * Remove all filters from manager. - */ - remove_all: function() { - this.filters = []; - this.parent_div.children().remove(); - }, - /** - * Initialize filters. - */ - init_filters: function() { - for (var i = 0; i < this.filters.length; i++) { - var filter = this.filters[i]; - filter.update_ui_elt(); - } - }, - /** - * Clear filters so that they do not impact track display. - */ - clear_filters: function() { - for (var i = 0; i < this.filters.length; i++) { - var filter = this.filters[i]; - filter.slider.slider("option", "values", [filter.min, filter.max]); - } - this.alpha_filter = null; - this.height_filter = null; - - // Hide icons for setting filters. - this.parent_div.find(".icon-button").hide(); - }, - run_on_dataset: function() { - // Get or create dictionary item. - var get_or_create_dict_item = function(dict, key, new_item) { - // Add new item to dict if - if (!(key in dict)) { - dict[key] = new_item; - } - return dict[key]; - }; - - // - // Find and group active filters. Active filters are those being used to hide data. - // Filters with the same tool id are grouped. - // - var active_filters = {}, - filter, - tool_filter_conditions; - for (var i = 0; i < this.filters.length; i++) { - filter = this.filters[i]; - if (filter.tool_id) { - // Add filtering conditions if filter low/high are set. - if (filter.min !== filter.low) { - tool_filter_conditions = get_or_create_dict_item(active_filters, filter.tool_id, []); - tool_filter_conditions[tool_filter_conditions.length] = filter.tool_exp_name + " >= " + filter.low; - } - if (filter.max !== filter.high) { - tool_filter_conditions = get_or_create_dict_item(active_filters, filter.tool_id, []); - tool_filter_conditions[tool_filter_conditions.length] = filter.tool_exp_name + " <= " + filter.high; - } - } - } - - // - // Use tools to run filters. - // - - // Create list of (tool_id, tool_filters) tuples. - var active_filters_list = []; - for (var tool_id in active_filters) { - active_filters_list[active_filters_list.length] = [tool_id, active_filters[tool_id]]; - } - - // Invoke recursive function to run filters; this enables chaining of filters via - // iteratively application. - (function run_filter(input_dataset_id, filters) { - var - // Set up filtering info and params. - filter_tuple = filters[0], - tool_id = filter_tuple[0], - tool_filters = filter_tuple[1], - tool_filter_str = "(" + tool_filters.join(") and (") + ")", - url_params = { - cond: tool_filter_str, - input: input_dataset_id, - target_dataset_id: input_dataset_id, - tool_id: tool_id - }, - // Remove current filter. - filters = filters.slice(1); - - $.getJSON(run_tool_url, url_params, function(response) { - if (response.error) { - // General error. - show_modal("Filter Dataset", - "Error running tool " + tool_id, - { "Close" : hide_modal } ); - } - else if (filters.length === 0) { - // No more filters to run. - show_modal("Filtering Dataset", - "Filter(s) are running on the complete dataset. Outputs are in dataset's history.", - { "Close" : hide_modal } ); - } - else { - // More filters to run. - run_filter(response.dataset_id, filters); - } - }); - - })(this.track.dataset_id, active_filters_list); - } -}); - -/** * Generates scale values based on filter and feature's value for filter. */ var FilterScaler = function(filter, default_val) { @@ -3224,7 +2612,7 @@ moveable(track.container_div, track.drag_handle_class, ".group", track); // Attribute init. - this.filters_manager = new FiltersManager(this, ('filters' in obj_dict ? obj_dict.filters : null)); + this.filters_manager = new filters.FiltersManager(this, ('filters' in obj_dict ? obj_dict.filters : null)); // HACK: set filters manager for data manager. // FIXME: prolly need function to set filters and update data_manager reference. this.data_manager.set('filters_manager', this.filters_manager); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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