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commit/galaxy-central: dannon: workflows api: patch from Tobias Wohlfrom <twohlfrom@illumina.com>
by Bitbucket 31 Mar '11

31 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/93ca67adcc56/ changeset: r5290:93ca67adcc56 user: dannon date: 2011-03-31 17:27:49 summary: workflows api: patch from Tobias Wohlfrom <twohlfrom(a)illumina.com> Fixed label output in workflow API in order to map the input datasets. affected #: 1 file (9 bytes) --- a/lib/galaxy/web/api/workflows.py Thu Mar 31 10:16:40 2011 -0400 +++ b/lib/galaxy/web/api/workflows.py Thu Mar 31 11:27:49 2011 -0400 @@ -57,7 +57,7 @@ inputs = {} for step in latest_workflow.steps: if step.type == 'data_input': - inputs[step.id] = {'label':"Input Dataset", 'value':""} + inputs[step.id] = {'label':step.tool_inputs['name'], 'value':""} else: pass # Eventually, allow regular tool parameters to be inserted and modified at runtime. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for wrapping input values for change_format and label tags when tool is using check_values="false". Fixes issue seen when e.g. using an output label in a data_source tool.
by Bitbucket 31 Mar '11

31 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b453988dce62/ changeset: r5289:b453988dce62 user: dan date: 2011-03-31 16:16:40 summary: Fix for wrapping input values for change_format and label tags when tool is using check_values="false". Fixes issue seen when e.g. using an output label in a data_source tool. affected #: 1 file (309 bytes) --- a/lib/galaxy/tools/actions/__init__.py Wed Mar 30 17:20:10 2011 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Thu Mar 31 10:16:40 2011 -0400 @@ -133,16 +133,18 @@ else: new_list.append( value ) return new_list - def wrap_values( inputs, input_values ): + def wrap_values( inputs, input_values, skip_missing_values = False ): # Wrap tool inputs as necessary for input in inputs.itervalues(): + if input.name not in input_values and skip_missing_values: + continue if isinstance( input, Repeat ): for d in input_values[ input.name ]: - wrap_values( input.inputs, d ) + wrap_values( input.inputs, d, skip_missing_values = skip_missing_values ) elif isinstance( input, Conditional ): values = input_values[ input.name ] current = values[ "__current_case__" ] - wrap_values( input.cases[current].inputs, values ) + wrap_values( input.cases[current].inputs, values, skip_missing_values = skip_missing_values ) elif isinstance( input, DataToolParameter ): input_values[ input.name ] = \ galaxy.tools.DatasetFilenameWrapper( input_values[ input.name ], @@ -254,7 +256,7 @@ if output.change_format: if params is None: params = make_dict_copy( incoming ) - wrap_values( tool.inputs, params ) + wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) for change_elem in output.change_format: for when_elem in change_elem.findall( 'when' ): check = when_elem.get( 'input', None ) @@ -304,7 +306,7 @@ # <outputs> # <data format="input" name="output" label="Blat on ${<input_param>.name}" /> # </outputs> - wrap_values( tool.inputs, params ) + wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) #tool (only needing to be set once) and on_string (set differently for each label) are overwritten for each output dataset label being determined params['tool'] = tool params['on_string'] = on_text 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: Send visual analytics output datasets to user's current history rather than input datasets' history. This enables users not logged in to use visual analytics in shared visualizations.
by Bitbucket 30 Mar '11

30 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/81b332adf892/ changeset: r5288:81b332adf892 user: jgoecks date: 2011-03-30 23:20:10 summary: Send visual analytics output datasets to user's current history rather than input datasets' history. This enables users not logged in to use visual analytics in shared visualizations. affected #: 1 file (11 bytes) --- a/lib/galaxy/web/controllers/tracks.py Wed Mar 30 11:44:08 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Wed Mar 30 17:20:10 2011 -0400 @@ -2,7 +2,7 @@ Support for constructing and viewing custom "track" browsers within Galaxy. """ -import re, time, pkg_resources +import re, pkg_resources pkg_resources.require( "bx-python" ) from bx.seq.twobit import TwoBitFile @@ -13,7 +13,6 @@ from galaxy.web.framework import simplejson from galaxy.web.framework.helpers import time_ago, grids from galaxy.util.bunch import Bunch -from galaxy import util from galaxy.datatypes.interval import Gff from galaxy.visualization.tracks.data_providers import * @@ -703,7 +702,8 @@ # Set input datasets for tool. Input datasets are subsets of full # datasets and are based on chrom, low, high. # - hda_permissions = trans.app.security_agent.history_get_default_permissions( original_dataset.history ) + job_history = trans.get_history( create=True ) + hda_permissions = trans.app.security_agent.history_get_default_permissions( job_history ) messages_list = [] for jida in original_job.input_datasets: input_dataset = jida.dataset @@ -721,7 +721,7 @@ name="Subset [%s:%i-%i] of data %i" % \ ( chrom, low, high, input_dataset.hid ), visible=False ) - input_dataset.history.add_dataset( subset_dataset ) + job_history.add_dataset( subset_dataset ) trans.sa_session.add( subset_dataset ) trans.app.security_agent.set_all_dataset_permissions( subset_dataset.dataset, hda_permissions ) @@ -744,7 +744,7 @@ # Start tool and handle outputs. # try: - subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=original_dataset.history ) + subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=job_history ) except Exception, e: # Lots of things can go wrong when trying to execute tool. return to_json_string( { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) } ) 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: add BED and GFF support to visual analytics framework, and enable GOPS intersect and subtract tools to work with visual analytics.
by Bitbucket 30 Mar '11

30 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e1f0a0dc1493/ changeset: r5287:e1f0a0dc1493 user: jgoecks date: 2011-03-30 17:44:08 summary: Trackster: add BED and GFF support to visual analytics framework, and enable GOPS intersect and subtract tools to work with visual analytics. affected #: 5 files (885 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Wed Mar 30 10:40:09 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Wed Mar 30 11:44:08 2011 -0400 @@ -487,8 +487,19 @@ col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } def write_data_to_file( self, chrom, start, end, filename ): - # TODO: write function. - pass + source = open( self.original_dataset.file_name ) + index = Indexes( self.converted_dataset.file_name ) + out = open( filename, 'w' ) + for start, end, offset in index.find(chrom, start, end): + source.seek( offset ) + if isinstance( self.original_dataset.datatype, Gff ): + reader = GFFReaderWrapper( source, fix_strand=True ) + feature = reader.next() + for interval in feature.intervals: + out.write(interval.raw_line + '\n') + elif isinstance( self.original_dataset.datatype, Bed ): + out.write( source.readline() ) + out.close() def get_filters( self ): """ Returns a dataset's filters. """ --- a/lib/galaxy/web/controllers/tracks.py Wed Mar 30 10:40:09 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Wed Mar 30 11:44:08 2011 -0400 @@ -724,9 +724,13 @@ input_dataset.history.add_dataset( subset_dataset ) trans.sa_session.add( subset_dataset ) trans.app.security_agent.set_all_dataset_permissions( subset_dataset.dataset, hda_permissions ) - if input_dataset.extension == 'bam': - data_provider = BamDataProvider( original_dataset=input_dataset, converted_dataset=converted_dataset ) - data_provider.write_data_to_file( chrom, low, high, subset_dataset.file_name ) + + # Write data subset to new HDA. + data_provider_class = get_data_provider( original_dataset=input_dataset ) + data_provider = data_provider_class( original_dataset=input_dataset, + converted_dataset=converted_dataset ) + data_provider.write_data_to_file( chrom, low, high, subset_dataset.file_name ) + # TODO: size not working. subset_dataset.set_size() subset_dataset.info = "Data subset for trackster" --- a/static/scripts/trackster.js Wed Mar 30 10:40:09 2011 -0400 +++ b/static/scripts/trackster.js Wed Mar 30 11:44:08 2011 -0400 @@ -1392,6 +1392,7 @@ // Slider. var slider_div = $("<div/>").addClass("slider").appendTo(param_div); var slider = $("<div id='" + param.name + "-param-control'>").appendTo(slider_div); + // Step must have a value so that (max-min)%step == 0. slider.slider({ min: param.min, max: param.max, --- a/tools/new_operations/intersect.xml Wed Mar 30 10:40:09 2011 -0400 +++ b/tools/new_operations/intersect.xml Wed Mar 30 11:44:08 2011 -0400 @@ -28,7 +28,7 @@ <param format="interval,gff" name="input2" type="data" help="Second dataset"><label>that intersect</label></param> - <param name="min" size="4" type="integer" value="1" help="(bp)"> + <param name="min" size="4" type="integer" value="1" min="0" max="600000" help="(bp)"><label>for at least</label></param></inputs> --- a/tools/new_operations/subtract.xml Wed Mar 30 10:40:09 2011 -0400 +++ b/tools/new_operations/subtract.xml Wed Mar 30 11:44:08 2011 -0400 @@ -31,7 +31,7 @@ <option value="-p">Non-overlapping pieces of intervals</option></param> - <param name="min" size="4" type="integer" value="1" help="(bp)"> + <param name="min" size="4" type="integer" value="1" min="0" max="600000" help="(bp)"><label>where minimal overlap is</label></param></inputs> 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: Minor fix for 5283:41a416e61021.
by Bitbucket 30 Mar '11

30 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3844b6d684b6/ changeset: r5286:3844b6d684b6 user: dan date: 2011-03-30 16:40:09 summary: Minor fix for 5283:41a416e61021. affected #: 1 file (4 bytes) --- a/lib/galaxy/datatypes/data.py Wed Mar 30 10:38:45 2011 -0400 +++ b/lib/galaxy/datatypes/data.py Wed Mar 30 10:40:09 2011 -0400 @@ -441,7 +441,7 @@ est_lines = self.estimate_file_lines(dataset) dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, self.line_class) ) else: - dataset.blurb = "%s %s" % util.commaify( str(line_count) ), inflector.cond_plural(line_count, self.line_class) + dataset.blurb = "%s %s" % ( util.commaify( str(line_count) ), inflector.cond_plural(line_count, self.line_class) ) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' 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: dannon: Removing a debug print from previous commit.
by Bitbucket 30 Mar '11

30 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/61036b55f4e4/ changeset: r5285:61036b55f4e4 user: dannon date: 2011-03-30 16:38:45 summary: Removing a debug print from previous commit. affected #: 1 file (25 bytes) --- a/lib/galaxy/datatypes/tabular.py Wed Mar 30 10:34:21 2011 -0400 +++ b/lib/galaxy/datatypes/tabular.py Wed Mar 30 10:38:45 2011 -0400 @@ -224,7 +224,6 @@ out.append( '%s</td></tr>' % escape( comments.pop(0) ) ) return "".join( out ) def set_peek( self, dataset, line_count=None, is_multi_byte=False): - print line_count super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte) if dataset.metadata.comment_lines: dataset.blurb = "%s, %s comments" % ( dataset.blurb, util.commaify( str( dataset.metadata.comment_lines ) ) ) 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: Minor fix for 5283:41a416e61021.
by Bitbucket 30 Mar '11

30 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/09d9091ec0a4/ changeset: r5284:09d9091ec0a4 user: dan date: 2011-03-30 16:34:21 summary: Minor fix for 5283:41a416e61021. affected #: 1 file (4 bytes) --- a/lib/galaxy/datatypes/data.py Wed Mar 30 07:14:20 2011 -0400 +++ b/lib/galaxy/datatypes/data.py Wed Mar 30 10:34:21 2011 -0400 @@ -436,7 +436,7 @@ #Small dataset, recount all lines and reset peek afterward. lc = self.count_data_lines(dataset) dataset.metadata.data_lines = lc - dataset.blurb = "%s %s" % util.commaify( str(lc) ), inflector.cond_plural(lc, self.line_class) + dataset.blurb = "%s %s" % ( util.commaify( str(lc) ), inflector.cond_plural(lc, self.line_class) ) else: est_lines = self.estimate_file_lines(dataset) dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, self.line_class) ) 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: dannon: Refactor set_peek to a single method in class Text. Should also fix bug introduced in 5236 that prevented setting of some metadata.
by Bitbucket 30 Mar '11

30 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/41a416e61021/ changeset: r5283:41a416e61021 user: dannon date: 2011-03-30 13:14:20 summary: Refactor set_peek to a single method in class Text. Should also fix bug introduced in 5236 that prevented setting of some metadata. affected #: 3 files (2.1 KB) --- a/lib/galaxy/datatypes/data.py Tue Mar 29 16:27:35 2011 -0400 +++ b/lib/galaxy/datatypes/data.py Wed Mar 30 07:14:20 2011 -0400 @@ -354,6 +354,7 @@ class Text( Data ): file_ext = 'txt' + line_class = 'line' """Add metadata elements""" MetadataElement( name="data_lines", default=0, desc="Number of data lines", readonly=True, optional=True, visible=False, no_value=0 ) @@ -417,26 +418,30 @@ data_lines += 1 return data_lines def set_peek( self, dataset, line_count=None, is_multi_byte=False ): + """ + Set the peek. This method is used by various subclasses of Text. + """ if not dataset.dataset.purged: # The file must exist on disk for the get_file_peek() method dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: # See if line_count is stored in the metadata - if dataset.metadata.data_lines is not None: - dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, "line") ) + if dataset.metadata.data_lines: + dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, self.line_class) ) else: # Number of lines is not known ( this should not happen ), and auto-detect is # needed to set metadata # This can happen when the file is larger than max_optional_metadata_filesize. if int(dataset.get_size()) <= 1048576: #Small dataset, recount all lines and reset peek afterward. - dataset.metadata.data_lines = self.count_data_lines(dataset) - self.set_peek(dataset) + lc = self.count_data_lines(dataset) + dataset.metadata.data_lines = lc + dataset.blurb = "%s %s" % util.commaify( str(lc) ), inflector.cond_plural(lc, self.line_class) else: est_lines = self.estimate_file_lines(dataset) - dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, "line") ) + dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, self.line_class) ) else: - dataset.blurb = "%s %s" % util.commaify( str(line_count) ), inflector.cond_plural(line_count, "line") + dataset.blurb = "%s %s" % util.commaify( str(line_count) ), inflector.cond_plural(line_count, self.line_class) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' --- a/lib/galaxy/datatypes/interval.py Tue Mar 29 16:27:35 2011 -0400 +++ b/lib/galaxy/datatypes/interval.py Wed Mar 30 07:14:20 2011 -0400 @@ -45,6 +45,7 @@ class Interval( Tabular ): """Tab delimited data containing interval information""" file_ext = "interval" + line_class = "region" """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) @@ -60,23 +61,6 @@ self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) def init_meta( self, dataset, copy_from=None ): Tabular.init_meta( self, dataset, copy_from=copy_from ) - def set_peek( self, dataset, line_count=None, is_multi_byte=False ): - """Set the peek and blurb text""" - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) - if line_count is None: - # See if line_count is stored in the metadata - if dataset.metadata.data_lines is not None: - dataset.blurb = "%s regions" % util.commaify( str( dataset.metadata.data_lines ) ) - else: - # Number of lines is not known ( this should not happen ), and auto-detect is - # needed to set metadata - dataset.blurb = "~%s regions" % util.commaify(util.roundify(str(self.estimate_file_lines(dataset)))) - else: - dataset.blurb = "%s regions" % util.commaify( str( line_count ) ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' def set_meta( self, dataset, overwrite = True, first_line_is_header = False, **kwd ): """Tries to guess from the line the location number of the column for the chromosome, region start-end and strand""" Tabular.set_meta( self, dataset, overwrite = overwrite, skip = 0 ) --- a/lib/galaxy/datatypes/tabular.py Tue Mar 29 16:27:35 2011 -0400 +++ b/lib/galaxy/datatypes/tabular.py Wed Mar 30 07:14:20 2011 -0400 @@ -223,8 +223,9 @@ out.append( '<tr><td>' ) out.append( '%s</td></tr>' % escape( comments.pop(0) ) ) return "".join( out ) - def set_peek( self, dataset, line_count=None, is_multi_byte=False ): - data.Text.set_peek( self, dataset, line_count=line_count, is_multi_byte=is_multi_byte ) + def set_peek( self, dataset, line_count=None, is_multi_byte=False): + print line_count + super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte) if dataset.metadata.comment_lines: dataset.blurb = "%s, %s comments" % ( dataset.blurb, util.commaify( str( dataset.metadata.comment_lines ) ) ) def display_peek( self, dataset ): @@ -383,6 +384,7 @@ class Pileup( Tabular ): """Tab delimited data in pileup (6- or 10-column) format""" file_ext = "pileup" + line_class = "genomic coordinate" """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) @@ -392,24 +394,6 @@ def init_meta( self, dataset, copy_from=None ): Tabular.init_meta( self, dataset, copy_from=copy_from ) - def set_peek( self, dataset, line_count=None, is_multi_byte=False ): - """Set the peek and blurb text""" - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) - if line_count is None: - # See if line_count is stored in the metadata - if dataset.metadata.data_lines is not None: - dataset.blurb = "%s genomic coordinates" % util.commaify( str( dataset.metadata.data_lines ) ) - else: - # Number of lines is not known ( this should not happen ), and auto-detect is - # needed to set metadata - dataset.blurb = "? genomic coordinates" - else: - dataset.blurb = "%s genomic coordinates" % util.commaify( str( line_count ) ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def make_html_table( self, dataset, skipchars=[] ): """Create HTML table, used for displaying peek""" out = ['<table cellspacing="0" cellpadding="3">'] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: simplify use of jQuery deferreds for getting data.
by Bitbucket 29 Mar '11

29 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7e383f2a3e6f/ changeset: r5282:7e383f2a3e6f user: jgoecks date: 2011-03-29 22:27:35 summary: Trackster: simplify use of jQuery deferreds for getting data. affected #: 1 file (448 bytes) --- a/static/scripts/trackster.js Tue Mar 29 14:28:17 2011 -0400 +++ b/static/scripts/trackster.js Tue Mar 29 16:27:35 2011 -0400 @@ -1071,6 +1071,15 @@ }); /** + * Tiles for TiledTracks. + */ +var Tile = function(track, canvas, histo_max) { + this.track = track; + this.canvas = canvas; + this.histo_max = histo_max; +}; + +/** * Tracks are objects can be added to the View. * * Track object hierarchy: @@ -1113,7 +1122,7 @@ this.content_div = $("<div class='track-content'>").appendTo(this.container_div); this.parent_element.append(this.container_div); }; -$.extend( Track.prototype, { +$.extend(Track.prototype, { /** * Initialize and draw the track. */ @@ -1476,7 +1485,7 @@ } */ }; -$.extend( TiledTrack.prototype, Track.prototype, { +$.extend(TiledTrack.prototype, Track.prototype, { /** * Make popup menu for track name. */ @@ -1732,23 +1741,17 @@ // Really draw tile: get data, seq data if available, and draw tile. // $.when(track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, - resolution, track.data_url_extra_params)).then(function() { - // Data available for track. - var result = track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, - resolution, track.data_url_extra_params); + resolution, track.data_url_extra_params)).then(function(tile_data) { // If sequence data needed, get that and draw. Otherwise draw. if (view.reference_track && w_scale > CHAR_WIDTH_PX) { $.when(view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, resolution, - view.reference_track.data_url_extra_params)).then(function() { - var seq_data = view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, - track.mode, resolution, - view.reference_track.data_url_extra_params); - draw_and_show_tile(id, result, resolution, tile_index, parent_element, w_scale, seq_data); + view.reference_track.data_url_extra_params)).then(function(seq_data) { + draw_and_show_tile(id, tile_data, resolution, tile_index, parent_element, w_scale, seq_data); }); } else { - draw_and_show_tile(id, result, resolution, tile_index, parent_element, w_scale); + draw_and_show_tile(id, tile_data, resolution, tile_index, parent_element, w_scale); } }); } 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 read id bug in Trackster BAM data provider.
by Bitbucket 29 Mar '11

29 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4a63c840c6ab/ changeset: r5281:4a63c840c6ab user: jgoecks date: 2011-03-29 20:28:17 summary: Fix read id bug in Trackster BAM data provider. affected #: 1 file (6 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Tue Mar 29 13:59:07 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Tue Mar 29 14:28:17 2011 -0400 @@ -306,12 +306,12 @@ if read.is_proper_pair: if qname in paired_pending: # one in dict is always first pair = paired_pending[qname] - results.append( [ "%i_%s" % ( read.pos, qname ), + results.append( [ "%i_%s" % ( pair['start'], qname ), pair['start'], read.pos + read_len, qname, [ pair['start'], pair['end'], pair['cigar'], pair['seq'] ], - [ read.pos, read.pos + read_len, read.cigar, seq] + [ read.pos, read.pos + read_len, read.cigar, seq ] ] ) del paired_pending[qname] else: 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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