April 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Visual analytics enhancements and fixes: (i) handle uncalled alleles in VCF display; (b) whitespace fixes; and (c) move methods so that non-feature tracks can be used when running tools; (d) fixes for SamDataProvider constructor; (e) fix for handling paired-end reads when using reference-based packing.
by commits-noreply＠bitbucket.org 16 Apr '13

16 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/64bb99fd3d3c/ Changeset: 64bb99fd3d3c User: jgoecks Date: 2013-04-16 15:24:45 Summary: Visual analytics enhancements and fixes: (i) handle uncalled alleles in VCF display; (b) whitespace fixes; and (c) move methods so that non-feature tracks can be used when running tools; (d) fixes for SamDataProvider constructor; (e) fix for handling paired-end reads when using reference-based packing. Affected #: 3 files diff -r b0a7fc043a9b24b28c0450839405cf534291352c -r 64bb99fd3d3cec9a65cc63ecfb0074ac5a87bd93 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -2,7 +2,7 @@ Data providers for genome visualizations. """ -import os, sys, operator, re +import os, sys, re from math import ceil, log import pkg_resources pkg_resources.require( "bx-python" ) @@ -696,12 +696,17 @@ has_alleles = False alleles_seen.clear() for allele in genotype_re.split( genotype ): - allele = int( allele ) - # Only count allele if it hasn't been seen yet. - if allele != 0 and allele not in alleles_seen: - allele_counts[ allele - 1 ] += 1 - alleles_seen[ allele ] = True - has_alleles = True + try: + # This may throw a ValueError if allele is missing. + allele = int( allele ) + + # Only count allele if it hasn't been seen yet. + if allele != 0 and allele not in alleles_seen: + allele_counts[ allele - 1 ] += 1 + alleles_seen[ allele ] = True + has_alleles = True + except ValueError: + pass # If no alleles, use empty string as proxy. if not has_alleles: @@ -1048,34 +1053,44 @@ # If there are results and reference data, transform read sequence and cigar. if len( results ) != 0 and ref_seq: + def process_read( read, start_field, cigar_field, seq_field ): + ''' + Process a read using the designated fields. + ''' + read_seq, read_cigar = get_ref_based_read_seq_and_cigar( read[ seq_field ].upper(), + read[ start_field ], + ref_seq, + start, + read[ cigar_field ] ) + read[ seq_field ] = read_seq + read[ cigar_field ] = read_cigar + def process_se_read( read ): ''' Process single-end read. ''' - read_seq, read_cigar = get_ref_based_read_seq_and_cigar( read[ 6 ].upper(), read[ 1 ], - ref_seq, start, read[ 4 ] ) - read[ 6 ] = read_seq - read[ 4 ] = read_cigar - + process_read( read, 1, 4, 6) + def process_pe_read( read ): ''' Process paired-end read. ''' - process_se_read( read[ 4 ] ) - process_se_read( read[ 5 ] ) + if len( read[4] ) > 2: + process_read( read[4], 0, 2, 4 ) + if len( read[5] ) > 2: + process_read( read[5], 0, 2, 4 ) # Uppercase for easy comparison. ref_seq = ref_seq.upper() - # Choose correct function for processing reads. - process_fn = process_se_read - if isinstance( results[ 0 ][ 5 ], list ): - process_fn = process_pe_read - # Process reads. for read in results: - process_fn( read ) - + # Use correct function for processing reads. + if isinstance( read[ 5 ], list ): + process_pe_read( read ) + else: + process_se_read( read ) + max_low, max_high = get_bounds( results, 1, 2 ) return { 'data': results, 'message': message, 'max_low': max_low, 'max_high': max_high } @@ -1086,14 +1101,16 @@ def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None ): """ Create SamDataProvider. """ + super( SamDataProvider, self ).__init__( converted_dataset=converted_dataset, + original_dataset=original_dataset, + dependencies=dependencies ) - # HACK: to use BamDataProvider, original dataset must be BAM and + # To use BamDataProvider, original dataset must be BAM and # converted dataset must be BAI. Use BAI from BAM metadata. if converted_dataset: + self.original_dataset = converted_dataset self.converted_dataset = converted_dataset.metadata.bam_index - self.original_dataset = converted_dataset - self.dependencies = dependencies - + class BBIDataProvider( GenomeDataProvider ): """ BBI data provider for the Galaxy track browser. diff -r b0a7fc043a9b24b28c0450839405cf534291352c -r 64bb99fd3d3cec9a65cc63ecfb0074ac5a87bd93 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -1660,7 +1660,10 @@ // Get variant to draw and set drawing properties. variant = null; if (genotype[0] === genotype[1]) { - if (genotype[0] !== '0') { + if (genotype[0] === '.') { + // TODO: draw uncalled variant. + } + else if (genotype[0] !== '0') { // Homozygous for variant. variant = alt[ parseInt(genotype[0], 10) - 1 ]; ctx.globalAlpha = 1; diff -r b0a7fc043a9b24b28c0450839405cf534291352c -r 64bb99fd3d3cec9a65cc63ecfb0074ac5a87bd93 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2421,15 +2421,18 @@ // Remove track. Drawable.prototype.action_icons_def[2] ], + can_draw: function() { if ( this.dataset_id && Drawable.prototype.can_draw.call(this) ) { return true; } return false; }, + build_container_div: function () { return $("<div/>").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); }, + build_header_div: function() { var header_div = $("<div class='track-header'/>"); if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(header_div); } @@ -2437,10 +2440,22 @@ .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); return header_div; }, + + /** + * Set track's dataset. + */ + set_dataset: function(dataset) { + this.dataset = dataset; + this.data_manager.set('dataset', dataset); + this.dataset_id = dataset.get('id'); + this.hda_ldda = dataset.get('hda_ldda'); + }, + /** * Action to take during resize. */ on_resize: function() {}, + /** * Add resizing handle to drawable's container_div. */ @@ -2477,6 +2492,7 @@ track.changed(); }).appendTo(track.container_div); }, + /** * Set track's modes and update mode icon popup. */ @@ -2508,6 +2524,7 @@ make_popupmenu(this.action_icons.mode_icon, mode_mapping); }, + build_action_icons: function() { Drawable.prototype.build_action_icons.call(this, this.action_icons_def); @@ -2516,6 +2533,7 @@ this.set_display_modes(this.display_modes); } }, + /** * Hide any elements that are part of the tracks contents area. Should * remove as approprite, the track will be redrawn by show_contents. @@ -2526,6 +2544,7 @@ // Hide any y axis labels (common to several track types) this.container_div.find(".yaxislabel, .track-resize").hide(); }, + show_contents: function() { // Show the contents div and labels (if present) this.tiles_div.show(); @@ -2533,6 +2552,7 @@ // Request a redraw of the content this.request_draw(); }, + /** * Returns track type. */ @@ -2561,6 +2581,7 @@ } return ""; }, + /** * Initialize and draw the track. */ @@ -2652,6 +2673,7 @@ this.update_icons(); return init_deferred; }, + /** * Additional initialization required before drawing track for the first time. */ @@ -3817,13 +3839,7 @@ this.set_painter_from_config(); }; extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, { - set_dataset: function(dataset) { - this.dataset_id = dataset.get('id'); - this.hda_ldda = dataset.get('hda_ldda'); - this.dataset = dataset; - this.data_manager.set('dataset', dataset); - }, - + set_painter_from_config: function() { if ( this.config.values['connector_style'] === 'arcs' ) { this.painter = painters.ArcLinkedFeaturePainter; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 16 Apr '13

16 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/460fd7d9cfe4/ Changeset: 460fd7d9cfe4 Branch: single-file-download User: BjoernGruening Date: 2013-04-06 16:33:11 Summary: enable single file downloads with 'download_by_url' Affected #: 1 file diff -r cb25513c63cd7aa2ebd472e91109c96276ed6d9d -r 460fd7d9cfe413e39c5257ff09e9bade88a71bb4 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -75,7 +75,7 @@ zip_archive_extracted = common_util.extract_zip( downloaded_file_path, work_dir ) dir = common_util.zip_extraction_directory( work_dir, downloaded_filename ) else: - dir = work_dir + dir = os.path.curdir elif action_type == 'shell_command': # <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> # Eliminate the shell_command clone action so remaining actions can be processed correctly. https://bitbucket.org/galaxy/galaxy-central/commits/b0a7fc043a9b/ Changeset: b0a7fc043a9b User: greg Date: 2013-04-16 15:04:35 Summary: Merged in BjoernGruening/galaxy-central-bgruening/single-file-download (pull request #151) enable single file downloads with 'download_by_url' Affected #: 1 file diff -r 8614ab445c993ebad66089af8b4e263acace5d39 -r b0a7fc043a9b24b28c0450839405cf534291352c lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -75,7 +75,7 @@ zip_archive_extracted = common_util.extract_zip( downloaded_file_path, work_dir ) dir = common_util.zip_extraction_directory( work_dir, downloaded_filename ) else: - dir = work_dir + dir = os.path.curdir elif action_type == 'shell_command': # <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> # Eliminate the shell_command clone action so remaining actions can be processed correctly. 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: richard_burhans: When dynamically generating SelectToolParameter options, if the data_meta filter is used and no 'from' source has been specified, set defaults for columns and largest_index if they have not already been set.
by commits-noreply＠bitbucket.org 15 Apr '13

15 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8614ab445c99/ Changeset: 8614ab445c99 User: richard_burhans Date: 2013-04-15 19:36:07 Summary: When dynamically generating SelectToolParameter options, if the data_meta filter is used and no 'from' source has been specified, set defaults for columns and largest_index if they have not already been set. Affected #: 1 file diff -r 5bd15f07491607c9774bc3b9b5db9a4aea25768b -r 8614ab445c993ebad66089af8b4e263acace5d39 lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -129,6 +129,13 @@ rval.append( fields ) return rval else: + if not self.dynamic_option.columns: + self.dynamic_option.columns = { + "name" : 0, + "value" : 1, + "selected" : 2 + } + self.dynamic_option.largest_index = 2 if not isinstance( meta_value, list ): meta_value = [meta_value] for value in meta_value: 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: Fix bug in Trackster that offset difference indication between bases instead of over bases.
by commits-noreply＠bitbucket.org 15 Apr '13

15 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5bd15f074916/ Changeset: 5bd15f074916 User: jgoecks Date: 2013-04-15 19:29:34 Summary: Fix bug in Trackster that offset difference indication between bases instead of over bases. Affected #: 1 file diff -r b9971c68e9472a021f5b7a6784ee1244a85d5a1f -r 5bd15f07491607c9774bc3b9b5db9a4aea25768b static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -864,7 +864,7 @@ } // Require a minimum w_scale so that variants are only drawn when somewhat zoomed in. else if (w_scale > 0.05) { - ctx.fillRect(c_start, + ctx.fillRect(c_start - gap, y_center + (pack_mode ? 1 : 4), Math.max( 1, Math.round(w_scale) ), (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); @@ -1172,7 +1172,7 @@ } // Require a minimum w_scale so that variants are only drawn when somewhat zoomed in. else if (w_scale > 0.05) { - ctx.fillRect(c_start, + ctx.fillRect(c_start - gap, y_center + (pack_mode ? 1 : 4), Math.max( 1, Math.round(w_scale) ), (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); 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: Trackster: enhance VCF track to show sample data and summary data and use base coloring.
by commits-noreply＠bitbucket.org 15 Apr '13

15 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9971c68e947/ Changeset: b9971c68e947 User: jgoecks Date: 2013-04-15 19:20:25 Summary: Trackster: enhance VCF track to show sample data and summary data and use base coloring. Affected #: 4 files diff -r 7e800d8223d95326cb956fbad0ee89e5a6e84f58 -r b9971c68e9472a021f5b7a6784ee1244a85d5a1f lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -552,7 +552,7 @@ return Tabular.make_html_table( self, dataset, column_names=self.column_names ) def get_track_type( self ): - return "VcfTrack", { "data": "tabix", "index": "summary_tree" } + return "VariantTrack", { "data": "tabix", "index": "summary_tree" } class Eland( Tabular ): """Support for the export.txt.gz file used by Illumina's ELANDv2e aligner""" diff -r 7e800d8223d95326cb956fbad0ee89e5a6e84f58 -r b9971c68e9472a021f5b7a6784ee1244a85d5a1f lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -2,7 +2,7 @@ Data providers for genome visualizations. """ -import os, sys, operator +import os, sys, operator, re from math import ceil, log import pkg_resources pkg_resources.require( "bx-python" ) @@ -601,12 +601,22 @@ """ Abstract class that processes VCF data from native format to payload format. - Payload format: TODO + Payload format: An array of entries for each locus in the file. Each array + has the following entries: + 1. GUID (unused) + 2. location (0-based) + 3. reference base(s) + 4. alternative base(s) + 5. quality score + 6. whether variant passed filter + 7. sample genotypes -- a single string with samples separated by commas; empty string + denotes the reference genotype + 8-end: allele counts for each alternative """ col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } - dataset_type = 'bai' + dataset_type = 'variant' def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): """ @@ -621,7 +631,7 @@ message - error/informative message """ - rval = [] + data = [] message = None def get_mapping( ref, alt ): @@ -651,6 +661,7 @@ return ref_in_alt_index, alt[ ref_in_alt_index + 1: ], [ [ cig_ops.find( "I" ), alt_len - ref_len ] ] # Pack data. + genotype_re = re.compile( '/|\|' ) for count, line in enumerate( iterator ): if count < start_val: continue @@ -658,37 +669,61 @@ message = self.error_max_vals % ( max_vals, "features" ) break + # Split line and aggregate data. feature = line.split() - start = int( feature[1] ) - 1 - ref = feature[3] - alts = feature[4] + pos, c_id, ref, alt, qual, c_filter, info = feature[ 1:8 ] + format = feature[ 8 ] + samples_data = feature [ 9: ] + # VCF is 1-based. + pos = int( pos ) - 1 + + # FIXME: OK to skip? + if alt == '.': + count -= 1 + continue - # HACK? alts == '.' --> monomorphism. - if alts == '.': - alts = ref + # Count number of samples matching each allele. + allele_counts = [ 0 for i in range ( alt.count( ',' ) + 1 ) ] - # Pack variants. - for alt in alts.split(","): - offset, new_seq, cigar = get_mapping( ref, alt ) - start += offset - end = start + len( new_seq ) + # Process and pack sample genotype. + sample_gts = [] + alleles_seen = {} + has_alleles = False - # Pack line. - payload = [ - hash( line ), - start, - end, - # ID: - feature[2], - cigar, - # TODO? VCF does not have strand, so default to positive. - "+", - new_seq, - None if feature[5] == '.' else float( feature[5] ) - ] - rval.append(payload) + for i, sample in enumerate( samples_data ): + # Parse and count alleles. + genotype = sample.split( ':' )[ 0 ] + has_alleles = False + alleles_seen.clear() + for allele in genotype_re.split( genotype ): + allele = int( allele ) + # Only count allele if it hasn't been seen yet. + if allele != 0 and allele not in alleles_seen: + allele_counts[ allele - 1 ] += 1 + alleles_seen[ allele ] = True + has_alleles = True + + # If no alleles, use empty string as proxy. + if not has_alleles: + genotype = '' - return { 'data': rval, 'message': message } + sample_gts.append( genotype ) + + # Add locus data. + locus_data = [ + -1, + pos, + c_id, + ref, + alt, + qual, + c_filter, + ','.join( sample_gts ) + ] + locus_data.extend( allele_counts ) + data.append( locus_data ) + + return { 'data': data, 'message': message } def write_data_to_file( self, regions, filename ): out = open( filename, "w" ) @@ -707,7 +742,8 @@ """ Provides data from a VCF file indexed via tabix. """ - pass + + dataset_type = 'variant' class RawVcfDataProvider( VcfDataProvider ): """ diff -r 7e800d8223d95326cb956fbad0ee89e5a6e84f58 -r b9971c68e9472a021f5b7a6784ee1244a85d5a1f static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -149,7 +149,7 @@ // Set base Y so that max label and data do not overlap. Base Y is where rectangle bases // start. However, height of each rectangle is relative to required_height; hence, the // max rectangle is required_height. - base_y = height; + base_y = height, delta_x_px = Math.ceil(this.data.delta * w_scale); ctx.save(); @@ -1285,7 +1285,7 @@ drawDownwardEquilateralTriangle(ctx, data[0], data[1], data[2]); } } - }, + } }); var ArcLinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) { @@ -1544,6 +1544,150 @@ ctx.restore(); }; +/** + * Paints variant data onto canvas. + */ +var VariantPainter = function(data, view_start, view_end, prefs, mode, base_color_fn) { + Painter.call(this, data, view_start, view_end, prefs, mode); + this.base_color_fn = base_color_fn; + this.divider_height = 1; +}; + +extend(VariantPainter.prototype, Painter.prototype, { + /** + * Height of a single row, depends on mode + */ + get_row_height: function() { + var mode = this.mode, height; + if (mode === "Dense") { + height = DENSE_TRACK_HEIGHT; + } + else if (mode === "Squish") { + height = SQUISH_TRACK_HEIGHT; + } + else { // mode === "Pack" + height = PACK_TRACK_HEIGHT; + } + return height; + }, + + get_required_height: function(rows_required, width) { + var height = this.prefs.summary_height; + if (this.prefs.show_sample_data) { + height += this.divider_height; + if (this.data.length !== 0) { + // Sample data is separated by commas, so this computes # of samples: + height += (this.data[0][7].match(/,/g).length + 1) * this.get_row_height(); + } + } + return height; + }, + + /** + * Draw on the context using a rectangle of width x height. w_scale is + * needed because it cannot be computed from width and view size alone + * as a left_offset may be present. + */ + draw: function(ctx, width, height, w_scale) { + var locus_data, + pos, + id, + ref, + alt, + qual, + filter, + sample_gts, + allele_counts, + variant, + draw_x_start, + char_x_start, + draw_y_start, + genotype, + // Always draw variants at least 1 pixel wide. + base_px = Math.max(1, Math.floor(w_scale)), + row_height = (this.mode === 'Squish' ? SQUISH_TRACK_HEIGHT : PACK_TRACK_HEIGHT), + // If zoomed out, fill the whole row with feature to make it easier to read; + // when zoomed in, use feature height so that there are gaps in sample rows. + feature_height = (w_scale < 0.1 ? + row_height : + (this.mode === 'Squish' ? SQUISH_FEATURE_HEIGHT : PACK_FEATURE_HEIGHT) + ), + j; + + // Draw divider between summary and samples. + if (this.prefs.show_sample_data) { + ctx.fillStyle = '#DDDDDD'; + ctx.globalAlpha = 1; + ctx.fillRect(0, this.prefs.summary_height - this.divider_height, width, this.divider_height); + } + + // Draw variants. + ctx.textAlign = "center"; + for (var i = 0; i < this.data.length; i++) { + // Get locus data. + locus_data = this.data[i]; + pos = locus_data[1]; + alt = locus_data[4].split(','); + sample_gts = locus_data[7].split(','); + allele_counts = locus_data.slice(8); + + // Compute start for drawing variants marker, text. + draw_x_start = Math.floor( Math.max(-0.5 * w_scale, (pos - this.view_start - 0.5) * w_scale) ); + char_x_start = Math.floor( Math.max(0, (pos - this.view_start) * w_scale) ); + + // Draw summary. + ctx.fillStyle = '#AAAAAA'; + // Draw background for summary. + ctx.fillRect(draw_x_start, 0, base_px, this.prefs.summary_height); + draw_y_start = this.prefs.summary_height; + // Draw allele fractions onto summary. + for (j = 0; j < alt.length; j++) { + ctx.fillStyle = this.base_color_fn(alt[j]); + allele_frac = allele_counts / sample_gts.length; + draw_height = Math.ceil(this.prefs.summary_height * allele_frac); + ctx.fillRect(draw_x_start, draw_y_start - draw_height, base_px, draw_height); + draw_y_start -= draw_height; + } + + // Done drawing if not showing samples data. + if (!this.prefs.show_sample_data) { continue; } + + // Draw sample genotypes. + draw_y_start = this.prefs.summary_height + this.divider_height; + for (j = 0; j < sample_gts.length; j++, draw_y_start += row_height) { + genotype = (sample_gts[j] ? sample_gts[j].split(/\/|\|/) : ['0', '0']); + + // Get variant to draw and set drawing properties. + variant = null; + if (genotype[0] === genotype[1]) { + if (genotype[0] !== '0') { + // Homozygous for variant. + variant = alt[ parseInt(genotype[0], 10) - 1 ]; + ctx.globalAlpha = 1; + } + // else reference + } + else { // Heterozygous for variant. + variant = (genotype[0] !== '0' ? genotype[0] : genotype[1]); + variant = alt[ parseInt(variant, 10) - 1 ]; + ctx.globalAlpha = 0.4; + } + + // If there's a variant, draw it. + if (variant) { + ctx.fillStyle = this.base_color_fn(variant); + if (this.mode === 'Squish' || w_scale < ctx.canvas.manager.char_width_px) { + ctx.fillRect(draw_x_start, draw_y_start + 1, base_px, feature_height); + } + else { + ctx.fillText(variant, char_x_start, draw_y_start + row_height); + } + } + } + } + } +}); + return { Scaler: Scaler, SummaryTreePainter: SummaryTreePainter, @@ -1552,7 +1696,8 @@ ReadPainter: ReadPainter, RefBasedReadPainter: RefBasedReadPainter, ArcLinkedFeaturePainter: ArcLinkedFeaturePainter, - DiagonalHeatmapPainter: DiagonalHeatmapPainter + DiagonalHeatmapPainter: DiagonalHeatmapPainter, + VariantPainter: VariantPainter }; diff -r 7e800d8223d95326cb956fbad0ee89e5a6e84f58 -r b9971c68e9472a021f5b7a6784ee1244a85d5a1f static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1712,7 +1712,7 @@ tool.run( // URL params. { - target_dataset_id: this.track.original_dataset_id, + target_dataset_id: this.track.dataset_id, action: 'rerun', tool_id: tool.id }, @@ -1741,7 +1741,7 @@ }), url_params = { - target_dataset_id: this.track.original_dataset_id, + target_dataset_id: this.track.dataset_id, action: 'rerun', tool_id: this.id, regions: [ @@ -2236,7 +2236,7 @@ * ----> ReferenceTrack * ----> FeatureTrack * -------> ReadTrack - * -------> VcfTrack + * ----> VariantTrack */ var Track = function(view, container, obj_dict) { // For now, track's container is always view. @@ -2251,7 +2251,9 @@ this.dataset = new data.Dataset({ id: obj_dict.dataset_id, hda_ldda: obj_dict.hda_ldda - }); + }); + this.dataset_id = this.dataset.get('id'); + this.hda_ldda = this.dataset.get('hda_ldda'); this.dataset_check_type = 'converted_datasets_state'; this.data_url_extra_params = {}; this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT); @@ -2548,8 +2550,8 @@ else if (this instanceof ReadTrack) { return "ReadTrack"; } - else if (this instanceof VcfTrack) { - return "VcfTrack"; + else if (this instanceof VariantTrack) { + return "VariantTrack"; } else if (this instanceof CompositeTrack) { return "CompositeTrack"; @@ -2679,6 +2681,7 @@ this.filters_available = false; this.tool = ('tool' in obj_dict && obj_dict.tool ? new Tool(this, obj_dict.tool, obj_dict.tool_state) : null); this.tile_cache = new visualization.Cache(TILE_CACHE_SIZE); + this.left_offset = 0; if (this.header_div) { // @@ -2917,8 +2920,9 @@ tile.html_elt.css("padding-top", ERROR_PADDING); } }); - } + } }, + /** * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a * jQuery.Deferred object that is fulfilled when tile can be drawn again. @@ -2967,7 +2971,7 @@ // HACK: this is FeatureTrack-specific. // If track mode is Auto, determine mode and update. var mode = track.mode; - if (mode === "Auto") { + if (mode === "Auto" && track.get_mode) { mode = track.get_mode(tile_data); track.update_auto_mode(mode); } @@ -3014,6 +3018,15 @@ }, /** + * Draw a track tile for summary tree data. + */ + _draw_summary_tree_tile: function(result, ctx, region, resolution, w_scale) { + var painter = new painters.SummaryTreePainter(result, region.get('start'), region.get('end'), this.prefs); + painter.draw(ctx, ctx.canvas.width, ctx.canvas.height, w_scale); + return new SummaryTreeTile(this, region, resolution, ctx.canvas, result.data, result.max); + }, + + /** * Draw a track tile. * @param result result from server * @param ctx canvas context to draw on @@ -3198,7 +3211,6 @@ // Init drawables; each drawable is a copy so that config/preferences // are independent of each other. Also init left offset. this.drawables = []; - this.left_offset = 0; if ('drawables' in obj_dict) { var drawable; for (var i = 0; i < obj_dict.drawables.length; i++) { @@ -3543,11 +3555,6 @@ this.mode = "Histogram"; TiledTrack.call(this, view, container, obj_dict); - this.hda_ldda = obj_dict.hda_ldda; - this.dataset_id = obj_dict.dataset_id; - this.original_dataset_id = this.dataset_id; - this.left_offset = 0; - // Define track configuration this.config = new DrawableConfig( { track: this, @@ -3690,12 +3697,6 @@ this.mode = "Heatmap"; TiledTrack.call(this, view, container, obj_dict); - // This all seems to be duplicated - this.hda_ldda = obj_dict.hda_ldda; - this.dataset_id = obj_dict.dataset_id; - this.original_dataset_id = this.dataset_id; - this.left_offset = 0; - // Define track configuration this.config = new DrawableConfig( { track: this, @@ -3746,12 +3747,11 @@ }, /** - * Draw LineTrack tile. + * Draw tile. */ draw_tile: function(result, ctx, mode, resolution, region, w_scale) { // Paint onto canvas. - var - canvas = ctx.canvas, + var canvas = ctx.canvas, painter = new painters.DiagonalHeatmapPainter(result.data, region.get('start'), region.get('end'), this.prefs, mode); painter.draw(ctx, canvas.width, canvas.height, w_scale); @@ -3806,9 +3806,6 @@ this.visible_height_px = this.config.values.height; this.container_div.addClass( "feature-track" ); - this.hda_ldda = obj_dict.hda_ldda; - this.dataset_id = obj_dict.dataset_id; - this.original_dataset_id = obj_dict.dataset_id; this.show_labels_scale = 0.001; this.showing_details = false; this.summary_draw_height = 30; @@ -3834,6 +3831,7 @@ this.painter = painters.LinkedFeaturePainter; } }, + /** * Actions to be taken before drawing. */ @@ -4053,10 +4051,7 @@ // Drawing the summary tree. if (mode === "summary_tree" || mode === "Coverage") { - // Paint summary tree into canvas - var painter = new painters.SummaryTreePainter(result, tile_low, tile_high, this.prefs); - painter.draw(ctx, canvas.width, canvas.height, w_scale); - return new SummaryTreeTile(track, region, resolution, canvas, result.data, result.max); + return this._draw_summary_tree_tile(result, ctx, region, resolution, w_scale); } // Handle row-by-row tracks @@ -4146,17 +4141,19 @@ } }); -var VcfTrack = function(view, container, obj_dict) { - FeatureTrack.call(this, view, container, obj_dict); +/** + * Track for displaying variant data. + */ +var VariantTrack = function(view, container, obj_dict) { + this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"]; + TiledTrack.call(this, view, container, obj_dict); this.config = new DrawableConfig( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, - { key: 'block_color', label: 'Block color', type: 'color', default_value: util.get_random_color() }, - { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, - { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false }, - { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true }, + { key: 'show_sample_data', label: 'Show sample data', type: 'bool', default_value: true }, + { key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true } ], saved_values: obj_dict.prefs, @@ -4168,10 +4165,54 @@ }); this.prefs = this.config.values; - this.painter = painters.ReadPainter; + this.painter = painters.VariantPainter; + this.summary_draw_height = 30; + + // Maximum resolution is ~45 pixels/base, so use this size left offset to ensure that full + // variant is drawn when variant is at start of tile. + this.left_offset = 30; }; -extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); +extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + /** + * Draw tile. + */ + draw_tile: function(result, ctx, mode, resolution, region, w_scale) { + // Data could be summary tree data or variant data. + if (result.dataset_type === 'summary_tree') { + return this._draw_summary_tree_tile(result, ctx, region, resolution, w_scale); + } + else { // result.dataset_type === 'variant' + var view = this.view, + painter = new (this.painter)(result.data, region.get('start'), region.get('end'), this.prefs, mode, + function(b) { return view.get_base_color(b); }); + painter.draw(ctx, ctx.canvas.width, ctx.canvas.height, w_scale); + return new Tile(this, region, resolution, ctx.canvas, result.data); + } + }, + + /** + * Returns canvas height needed to display data; return value is an integer that denotes the + * number of pixels required. + */ + get_canvas_height: function(result, mode, w_scale, canvas_width) { + if (result.dataset_type === 'summary_tree') { + return this.summary_draw_height; + } + else { + var dummy_painter = new (this.painter)(result.data, null, null, this.prefs, mode); + return dummy_painter.get_required_height(); + } + }, + + /** + * Actions to be taken before drawing. + */ + before_draw: function() { + // Clear because this is set when drawing. + this.max_height_px = 0; + } +}); /** * Track that displays mapped reads. Track expects position data in 1-based, closed format, i.e. SAM/BAM format. @@ -4214,14 +4255,16 @@ /** * Objects that can be added to a view. */ -var addable_objects = { +var addable_objects = { + "CompositeTrack": CompositeTrack, + "DrawableGroup": DrawableGroup, + "DiagonalHeatmapTrack": DiagonalHeatmapTrack, + "FeatureTrack": FeatureTrack, "LineTrack": LineTrack, - "FeatureTrack": FeatureTrack, - "VcfTrack": VcfTrack, "ReadTrack": ReadTrack, - "DiagonalHeatmapTrack": DiagonalHeatmapTrack, - "CompositeTrack": CompositeTrack, - "DrawableGroup": DrawableGroup + "VariantTrack": VariantTrack, + // For backward compatibility, map vcf track to variant. + "VcfTrack": VariantTrack }; /** @@ -4252,7 +4295,7 @@ FeatureTrack: FeatureTrack, DiagonalHeatmapTrack: DiagonalHeatmapTrack, ReadTrack: ReadTrack, - VcfTrack: VcfTrack, + VariantTrack: VariantTrack, CompositeTrack: CompositeTrack, object_from_template: object_from_template }; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 15 Apr '13

15 Apr '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/242cd6a9b919/ Changeset: 242cd6a9b919 User: jmchilton Date: 2013-04-08 22:43:33 Summary: For even the most vanilla multiple selection tool parameters, if no option is selected and the tool is rerun the GUI indicates "An invalid option was selected, please verify" with a scary red box even though the tool will run fine. I feel there must be a cleaner way to address this, but it would probably be very invasive. Affected #: 1 file diff -r 788cd3d065413b2611d82375a5d0d562775ea529 -r 242cd6a9b919a5b47b2405bdabe94317e8008614 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -712,6 +712,8 @@ rval.append( v ) return rval else: + if self.multiple and value == "None" and "None" not in legal_values: + return [] if value not in legal_values: raise ValueError( "An invalid option was selected, please verify" ) return value https://bitbucket.org/galaxy/galaxy-central/commits/32b5ba798a39/ Changeset: 32b5ba798a39 User: jmchilton Date: 2013-04-15 01:59:13 Summary: Allow non-optional multiple select tool parameters. Affected #: 1 file diff -r 242cd6a9b919a5b47b2405bdabe94317e8008614 -r 32b5ba798a39d9a8169514614013fc5b2225edf3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -623,6 +623,8 @@ def __init__( self, tool, elem, context=None ): ToolParameter.__init__( self, tool, elem ) self.multiple = string_as_bool( elem.get( 'multiple', False ) ) + # Multiple selects are optional by default, single selection is the inverse. + self.optional = string_as_bool( elem.get( 'optional', self.multiple ) ) self.display = elem.get( 'display', None ) self.separator = elem.get( 'separator', ',' ) self.legal_values = set() @@ -712,8 +714,13 @@ rval.append( v ) return rval else: - if self.multiple and value == "None" and "None" not in legal_values: - return [] + value_is_none = ( value == "None" and "None" not in legal_values ) + if value_is_none: + if self.multiple: + if self.optional: + return [] + else: + raise ValueError( "No option was selected but input is not optional." ) if value not in legal_values: raise ValueError( "An invalid option was selected, please verify" ) return value https://bitbucket.org/galaxy/galaxy-central/commits/7e800d8223d9/ Changeset: 7e800d8223d9 User: dan Date: 2013-04-15 19:13:35 Summary: Merged in jmchilton/galaxy-central-multi-input-tool-fixes-2 (pull request #154) Fix for empty multiple selections Affected #: 1 file diff -r ad1ad2e1cce31b1d4f916633970e8a39d54067eb -r 7e800d8223d95326cb956fbad0ee89e5a6e84f58 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -623,6 +623,8 @@ def __init__( self, tool, elem, context=None ): ToolParameter.__init__( self, tool, elem ) self.multiple = string_as_bool( elem.get( 'multiple', False ) ) + # Multiple selects are optional by default, single selection is the inverse. + self.optional = string_as_bool( elem.get( 'optional', self.multiple ) ) self.display = elem.get( 'display', None ) self.separator = elem.get( 'separator', ',' ) self.legal_values = set() @@ -712,6 +714,13 @@ rval.append( v ) return rval else: + value_is_none = ( value == "None" and "None" not in legal_values ) + if value_is_none: + if self.multiple: + if self.optional: + return [] + else: + raise ValueError( "No option was selected but input is not optional." ) if value not in legal_values: raise ValueError( "An invalid option was selected, please verify" ) return value Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Close catless-file-merge branch.
by commits-noreply＠bitbucket.org 15 Apr '13

15 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/97776a49c3ed/ Changeset: 97776a49c3ed Branch: catless-file-merge User: dan Date: 2013-04-15 19:09:25 Summary: Close catless-file-merge branch. Affected #: 0 files 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: Browser tests: fix to timeout length in waitForNavigation, change display button tooltip text, cleanup
by commits-noreply＠bitbucket.org 15 Apr '13

15 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ad1ad2e1cce3/ Changeset: ad1ad2e1cce3 User: carlfeberhard Date: 2013-04-15 17:21:14 Summary: Browser tests: fix to timeout length in waitForNavigation, change display button tooltip text, cleanup Affected #: 5 files diff -r 388e86c30bad627de5aecb41675d5b35051d9e1d -r ad1ad2e1cce31b1d4f916633970e8a39d54067eb test/casperjs/anon-history-tests.js --- a/test/casperjs/anon-history-tests.js +++ b/test/casperjs/anon-history-tests.js @@ -68,45 +68,43 @@ }); // ------------------------------------------------------------------- check the empty history for well formedness -spaceghost.thenOpen( spaceghost.baseUrl, function testPanelStructure(){ +spaceghost.historypanel.waitForHdas( function testPanelStructure(){ this.test.comment( 'history panel for anonymous user, new history' ); - this.withHistoryPanel( function(){ - this.test.comment( "frame should have proper url and title: 'History'" ); - this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); - this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); + this.test.comment( "frame should have proper url and title: 'History'" ); + this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); + this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); - this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); - this.test.assertExists( nameSelector, nameSelector + ' exists' ); - this.test.assertVisible( nameSelector, 'History name is visible' ); - this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); + this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); + this.test.assertExists( nameSelector, nameSelector + ' exists' ); + this.test.assertVisible( nameSelector, 'History name is visible' ); + this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); - this.test.comment( "history subtitle should display size and size should be 0 bytes" ); - this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); - this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); - this.test.assertSelectorHasText( subtitleSelector, initialSizeStr, - 'History subtitle has "' + initialSizeStr + '"' ); + this.test.comment( "history subtitle should display size and size should be 0 bytes" ); + this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); + this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); + this.test.assertSelectorHasText( subtitleSelector, initialSizeStr, + 'History subtitle has "' + initialSizeStr + '"' ); - this.test.comment( "NO tags or annotations icons should be available for an anonymous user" ); - this.test.assertDoesntExist( tagIconSelector, 'Tag icon button not found' ); - this.test.assertDoesntExist( annoIconSelector, 'Annotation icon button not found' ); + this.test.comment( "NO tags or annotations icons should be available for an anonymous user" ); + this.test.assertDoesntExist( tagIconSelector, 'Tag icon button not found' ); + this.test.assertDoesntExist( annoIconSelector, 'Annotation icon button not found' ); - this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); - this.test.comment( "A message about the current history being empty should be displayed" ); - this.test.assertVisible( emptyMsgSelector, 'Empty history message is visible' ); - this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, - 'Message contains "' + emptyMsgStr + '"' ); + this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); + this.test.comment( "A message about the current history being empty should be displayed" ); + this.test.assertVisible( emptyMsgSelector, 'Empty history message is visible' ); + this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, + 'Message contains "' + emptyMsgStr + '"' ); - this.test.comment( 'name should have a tooltip with info on anon-user name editing' ); - this.historypanel.hoverOver( nameSelector ); - this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); - this.test.assertSelectorHasText( tooltipSelector, anonNameTooltip ); + this.test.comment( 'name should have a tooltip with info on anon-user name editing' ); + this.historypanel.hoverOver( nameSelector ); + this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); + this.test.assertSelectorHasText( tooltipSelector, anonNameTooltip ); - this.test.comment( 'name should NOT be editable when clicked by anon-user' ); - this.assertDoesntHaveClass( nameSelector, editableTextClass, "Name field is not classed as editable text" ); - this.click( nameSelector ); - this.test.assertDoesntExist( editableTextInput, "Clicking on name does not create an input" ); - }); + this.test.comment( 'name should NOT be editable when clicked by anon-user' ); + this.assertDoesntHaveClass( nameSelector, editableTextClass, "Name field is not classed as editable text" ); + this.click( nameSelector ); + this.test.assertDoesntExist( editableTextInput, "Clicking on name does not create an input" ); }); // ------------------------------------------------------------------- anon user can upload file diff -r 388e86c30bad627de5aecb41675d5b35051d9e1d -r ad1ad2e1cce31b1d4f916633970e8a39d54067eb test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -50,6 +50,13 @@ options = options || {}; options.async = false; + // PUT data needs to be stringified in jq.ajax and the content changed + //TODO: server side handling could change this? + if( ( options.type && options.type === 'PUT' ) && ( options.data ) ){ + options.contentType = 'application/json'; + options.data = JSON.stringify( options.data ); + } + this.ensureJQuery( '../../static/scripts/libs/jquery/jquery.js' ); var resp = this.spaceghost.evaluate( function( url, options ){ return jQuery.ajax( url, options ); @@ -189,10 +196,8 @@ HDAAPI.prototype.urlTpls = { index : 'api/histories/%s/contents', show : 'api/histories/%s/contents/%s', - create : 'api/histories/%s/contents'//, - // not implemented - //delete_ : 'api/histories/%s', - //undelete: 'api/histories/deleted/%s/undelete' + create : 'api/histories/%s/contents', + update : 'api/histories/%s/contents/%s' }; HDAAPI.prototype.index = function index( historyId, ids ){ @@ -213,7 +218,7 @@ id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); deleted = deleted || false; - return this.api._ajax( utils.format( this.urlTpls.show, id ), { + return this.api._ajax( utils.format( this.urlTpls.show, this.api.ensureId( historyId ), id ), { data : { deleted: deleted } }); }; @@ -223,9 +228,24 @@ // py.payload <-> ajax.data payload = this.api.ensureObject( payload ); - return this.api._ajax( utils.format( this.urlTpls.create ), { + return this.api._ajax( utils.format( this.urlTpls.create, this.api.ensureId( historyId ) ), { type : 'POST', data : payload }); }; +HDAAPI.prototype.update = function create( historyId, id, payload ){ + this.api.spaceghost.info( 'history.update: ' + this.api.spaceghost.jsonStr( payload ) ); + + // py.payload <-> ajax.data + historyId = this.api.ensureId( historyId ); + id = this.api.ensureId( id ); + payload = this.api.ensureObject( payload ); + url = utils.format( this.urlTpls.update, historyId, id ); + + return this.api._ajax( url, { + type : 'PUT', + data : payload + }); +}; + diff -r 388e86c30bad627de5aecb41675d5b35051d9e1d -r ad1ad2e1cce31b1d4f916633970e8a39d54067eb test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -315,7 +315,7 @@ // mixing text and selectors here display : { selector : '.icon-button.display', - tooltip : 'Display data in browser', + tooltip : 'View data', hrefTpl : '/datasets/%s/display', nodeName : 'a' }, diff -r 388e86c30bad627de5aecb41675d5b35051d9e1d -r ad1ad2e1cce31b1d4f916633970e8a39d54067eb test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -1,11 +1,4 @@ // =================================================================== module object, exports -/** Creates a new user module object. - * @exported - */ -exports.create = function createUser( spaceghost ){ - return new User( spaceghost ); -}; - /** User object constructor. * @param {SpaceGhost} spaceghost a spaceghost instance */ @@ -15,6 +8,13 @@ }; exports.User = User; +/** Creates a new user module object. + * @exported + */ +exports.create = function createUser( spaceghost ){ + return new User( spaceghost ); +}; + User.prototype.toString = function toString(){ return this.spaceghost + '.User'; }; diff -r 388e86c30bad627de5aecb41675d5b35051d9e1d -r ad1ad2e1cce31b1d4f916633970e8a39d54067eb test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -551,6 +551,7 @@ }; /** Wait for a multiple navigation requests then call a function. + * NOTE: waitFor time is set to <number of urls> * options.waitTimeout * NOTE: uses string indexOf - doesn't play well with urls like [ 'history', 'history/bler' ] * @param {String[]} urlsToWaitFor the relative urls to wait for * @param {Function} then the function to call after the nav request @@ -563,7 +564,7 @@ function catchNavReq( url ){ //this.debug( 'nav.req: ' + url ); - for( var i=( urlsToWaitFor.length - 1 ); i>=0; i-- ){ + for( var i=( urlsToWaitFor.length - 1 ); i>=0; i -= 1 ){ //this.debug( '\t checking: ' + urlsToWaitFor[i] ); if( urlMatches( urlsToWaitFor[i], url ) ){ this.info( 'Navigation (' + urlsToWaitFor[i] + ') found: ' + url ); @@ -584,7 +585,8 @@ }, function callThen(){ if( utils.isFunction( then ) ){ then.call( this ); } - } + }, + this.options.waitTimeout * urlsToWaitFor.length ); return this; }; @@ -779,7 +781,7 @@ //TODO: * @param {Boolean} removeOtherListeners option to remove other listeners while this fires var spaceghost = this; function testTheError( msg, backtrace ){ - spaceghost.test.assert( msg.indexOf( msgContains ) != -1, 'Raised correct error: ' + msg ); + spaceghost.test.assert( msg.indexOf( msgContains ) !== -1, 'Raised correct error: ' + msg ); } this.tryStepsCatch( stepsFn, testTheError ); }; @@ -824,7 +826,7 @@ * @param {String} className the class to test for (classes passed in with a leading '.' will have it trimmed) */ SpaceGhost.prototype.assertHasClass = function assertHasClass( selector, className, msg ){ - className = ( className[0] == '.' )?( className.slice( 1 ) ):( className ); + className = ( className[0] === '.' )?( className.slice( 1 ) ):( className ); msg = msg || 'selector "' + selector + '" has class: "' + className + '"'; var classes = this.getElementAttribute( selector, 'class' ); this.test.assert( classes.indexOf( className ) !== -1, msg ); @@ -835,7 +837,7 @@ * @param {String} className the class to test for (classes passed in with a leading '.' will have it trimmed) */ SpaceGhost.prototype.assertDoesntHaveClass = function assertDoesntHaveClass( selector, className, msg ){ - className = ( className[0] == '.' )?( className.slice( 1 ) ):( className ); + className = ( className[0] === '.' )?( className.slice( 1 ) ):( className ); msg = msg || 'selector "' + selector + '" has class: "' + className + '"'; var classes = this.getElementAttribute( selector, 'class' ); this.test.assert( classes.indexOf( className ) === -1, msg ); @@ -908,6 +910,7 @@ count -= 1; if( count <= 0 ){ clearInterval( interval ); } }, delay ); + return this; }; /** Pop all handlers for eventName from casper and return them in order. 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: inithello: Fix for tool listing with run_functional_tests.sh -list, contributed by Peter Cock.
by commits-noreply＠bitbucket.org 15 Apr '13

15 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/388e86c30bad/ Changeset: 388e86c30bad User: inithello Date: 2013-04-15 16:09:51 Summary: Fix for tool listing with run_functional_tests.sh -list, contributed by Peter Cock. Affected #: 1 file diff -r 686781f9a8de43b74c19eb8282e47e6bc75342dd -r 388e86c30bad627de5aecb41675d5b35051d9e1d tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -35,14 +35,15 @@ for line in open("tools/"+tool) : if line.find("<tool ") != -1 and line.find("id") != -1 : keys = line.strip().split('\"') - n = 0 tool_info = dict() tool_info["desc"] = '' - while n < len(keys) : - if keys[n].find("id") != -1 : tool_info["id"] = keys[n+1].replace(' ', '_') - if keys[n].find("name") != -1 : tool_info["name"] = keys[n+1] - if keys[n].find("description") != -1 : tool_info["desc"] = keys[n+1] - n = n + 1 + for n in range(len(keys)-1): + if " id=" in keys[n]: + tool_info["id"] = keys[n+1].replace(' ', '_') + if " name=" in keys[n]: + tool_info["name"] = keys[n+1] + if " description=" in keys[n]: + tool_info["desc"] = keys[n+1] tool_infos.append(tool_info) break Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Apr '13

15 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/510b063792de/ Changeset: 510b063792de Branch: catless-file-merge User: BjoernGruening Date: 2013-03-22 17:05:51 Summary: Change file-merging to use copy.copyfileobj() rather than cat and mv. Affected #: 1 file diff -r d629a346b859c91ba0da27f865952580d1054d80 -r 510b063792de89332428ed12ea1025155a7769c9 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -544,21 +544,21 @@ return False - def merge( split_files, output_file): """ - TODO: Do we need to merge gzip files using gzjoin? cat seems to work, - but might be brittle. Need to revisit this. + Merge files with copy.copyfileobj() will not hit the + max argument limitation of cat. gz and bz2 files are also working. """ if not split_files: raise ValueError('Asked to merge zero files as %s' % output_file) elif len(split_files) == 1: - cmd = 'mv -f %s %s' % ( split_files[0], output_file ) + shutil.copyfileobj(open(split_files[0], 'rb'), open(output_file, 'wb')) else: - cmd = 'cat %s > %s' % ( ' '.join(split_files), output_file ) - result = os.system(cmd) - if result != 0: - raise Exception('Result %s from %s' % (result, cmd)) + fdst = open(output_file, 'wb') + for fsrc in split_files: + shutil.copyfileobj(open(fsrc, 'rb'), fdst) + fdst.close() + merge = staticmethod(merge) def get_visualizations( self, dataset ): https://bitbucket.org/galaxy/galaxy-central/commits/686781f9a8de/ Changeset: 686781f9a8de User: dannon Date: 2013-04-15 16:03:15 Summary: Merged in BjoernGruening/galaxy-central-bgruening/catless-file-merge (pull request #141) Change file-merging to use copy.copyfileobj() rather than cat and mv. Affected #: 1 file diff -r 3dd4b4a9221c8a839ad80f61cade10ac6480192b -r 686781f9a8de43b74c19eb8282e47e6bc75342dd lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -539,21 +539,21 @@ return False - def merge( split_files, output_file): """ - TODO: Do we need to merge gzip files using gzjoin? cat seems to work, - but might be brittle. Need to revisit this. + Merge files with copy.copyfileobj() will not hit the + max argument limitation of cat. gz and bz2 files are also working. """ if not split_files: raise ValueError('Asked to merge zero files as %s' % output_file) elif len(split_files) == 1: - cmd = 'mv -f %s %s' % ( split_files[0], output_file ) + shutil.copyfileobj(open(split_files[0], 'rb'), open(output_file, 'wb')) else: - cmd = 'cat %s > %s' % ( ' '.join(split_files), output_file ) - result = os.system(cmd) - if result != 0: - raise Exception('Result %s from %s' % (result, cmd)) + fdst = open(output_file, 'wb') + for fsrc in split_files: + shutil.copyfileobj(open(fsrc, 'rb'), fdst) + fdst.close() + merge = staticmethod(merge) def get_visualizations( self, dataset ): 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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