1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/384f3b803e64/ changeset: r5044:384f3b803e64 user: kanwei date: 2011-02-11 06:53:49 summary: trackster: Properly return NO_DATA for LineTrack datasets, fix error when no data is available affected #: 3 files (329 bytes)

--- a/lib/galaxy/datatypes/interval.py Thu Feb 10 17:43:39 2011 -0500 +++ b/lib/galaxy/datatypes/interval.py Fri Feb 11 00:53:49 2011 -0500 @@ -1161,7 +1161,7 @@ resolution = max( resolution, 1 ) return resolution def get_track_type( self ): - return "LineTrack", {"data": "bigwig"} + return "LineTrack", {"data": "bigwig", "index": "bigwig"}

class CustomTrack ( Tabular ): """UCSC CustomTrack"""

--- a/lib/galaxy/visualization/tracks/data_providers.py Thu Feb 10 17:43:39 2011 -0500 +++ b/lib/galaxy/visualization/tracks/data_providers.py Fri Feb 11 00:53:49 2011 -0500 @@ -48,13 +48,13 @@ # Override. pass

- def has_data( self, chrom, start, end ): + def has_data( self, chrom, start, end, **kwargs ): """ Returns true if dataset has data in the specified genome window, false otherwise. """ # Override. - return False + pass

def get_data( self, chrom, start, end, **kwargs ): """ Returns data in region defined by chrom, start, and end. """ @@ -140,10 +140,9 @@ else: return results, stats[level]["max"], stats[level]["avg"], stats[level]["delta"]

- def has_data( self, chrom, start, end ): + def has_data( self, chrom ): """ - Returns true if dataset has data in the specified genome window, false - otherwise. + Returns true if dataset has data for this chrom """

# Get summary tree. @@ -154,8 +153,7 @@ self.CACHE[filename] = st

# Check for data. - level = ceil( log( 100000, st.block_size ) ) - 1 - return ( st.query( chrom, int(start), int(end), level ) is not None ) + return st.chrom_blocks.get(chrom, None) is not None

class VcfDataProvider( TracksDataProvider ): """ @@ -405,14 +403,24 @@ """ BigWig data provider for the Galaxy track browser. """ - - def get_data( self, chrom, start, end, **kwargs ): - # Bigwig has the possibility of it being a standalone bigwig file, in which case we use - # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset + def _get_dataset( self ): if self.converted_dataset is not None: f = open( self.converted_dataset.file_name ) else: f = open( self.original_dataset.file_name ) + return f + + def has_data( self, chrom ): + f = self._get_dataset() + bw = BigWigFile(file=f) + all_dat = bw.query(chrom, 0, 2147483647, 1) + f.close() + return all_dat is not None + + def get_data( self, chrom, start, end, **kwargs ): + # Bigwig has the possibility of it being a standalone bigwig file, in which case we use + # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset + f = self._get_dataset() bw = BigWigFile(file=f)

if 'stats' in kwargs: @@ -426,7 +434,6 @@ 'min': float( all_dat['min'] ), \ 'total_frequency': float( all_dat['coverage'] ) }

- start = int(start) end = int(end) num_points = 2000 @@ -439,9 +446,10 @@ pos = start step_size = (end - start) / num_points result = [] - for dat_dict in data: - result.append( (pos, float_nan(dat_dict['mean']) ) ) - pos += step_size + if data: + for dat_dict in data: + result.append( (pos, float_nan(dat_dict['mean']) ) ) + pos += step_size

return result

--- a/lib/galaxy/web/controllers/tracks.py Thu Feb 10 17:43:39 2011 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Fri Feb 11 00:53:49 2011 -0500 @@ -458,13 +458,17 @@ return msg

# Check for data in the genome window. - # TODO: Not all tracks have an index data source, so need to try alternative data sources to check for data. - if chrom and low and high and data_sources.get( 'index' ): + if data_sources.get( 'index' ): tracks_dataset_type = data_sources['index']['name'] indexer = get_data_provider( tracks_dataset_type )( dataset.get_converted_dataset( trans, tracks_dataset_type ), dataset ) - if not indexer.has_data( chrom, low, high ): + if not indexer.has_data( chrom ): return messages.NO_DATA - + else: + # Standalone data provider + standalone_provider = get_data_provider(data_sources['data_standalone']['name'])( dataset ) + kwargs = {"stats": True} + if not standalone_provider.has_data( chrom ): + return messages.NO_DATA return messages.DATA

@web.json

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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