2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/97338d705f3a/ changeset: 97338d705f3a user: jgoecks date: 2012-06-04 05:07:54 summary: Fix import to be compatible with previous changeset. affected #: 1 file diff -r 4051e35d4cfd4f0f692b392553d9d99c9f388724 -r 97338d705f3acb4baa4e2f4d460c74fd8dde5761 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -15,7 +15,7 @@ from galaxy.datatypes.interval import Gff, Bed from galaxy.model import NoConverterException, ConverterDependencyException from galaxy.visualization.tracks.data_providers import * -from galaxy.visualization.tracks.genomes import decode_dbkey, Genomes +from galaxy.visualization.genomes import decode_dbkey, Genomes from galaxy.visualization.tracks.visual_analytics import get_tool_def, get_dataset_job # Message strings returned to browser https://bitbucket.org/galaxy/galaxy-central/changeset/44cc39cf2bd4/ changeset: 44cc39cf2bd4 user: jgoecks date: 2012-06-04 05:09:08 summary: Merge affected #: 1 file diff -r 97338d705f3acb4baa4e2f4d460c74fd8dde5761 -r 44cc39cf2bd41154aa1573e253b87f77ec97ae99 lib/galaxy/visualization/genomes.py --- a/lib/galaxy/visualization/genomes.py +++ b/lib/galaxy/visualization/genomes.py @@ -32,47 +32,12 @@ self.key = key self.len_file = len_file self.twobit_file = twobit_file - - -class Genomes( object ): - """ - Provides information about available genome data and methods for manipulating that data. - """ - - def __init__( self, app ): - # Create list of known genomes from len files. - self.genomes = {} - len_files = glob.glob( os.path.join( app.config.len_file_path, "*.len" ) ) - for f in len_files: - key = os.path.split( f )[1].split( ".len" )[0] - self.genomes[ key ] = Genome( key, len_file=f ) - - # Add genome data (twobit files) to genomes. - for line in open( os.path.join( app.config.tool_data_path, "twobit.loc" ) ): - if line.startswith("#"): continue - val = line.split() - if len( val ) == 2: - key, path = val - if key in self.genomes: - self.genomes[ key ].twobit_file = path - - def get_dbkeys_with_chrom_info( self, trans ): - """ Returns all valid dbkeys that have chromosome information. """ - - # All user keys have a len file. - user_keys = {} - user = trans.get_user() - if 'dbkeys' in user.preferences: - user_keys = from_json_string( user.preferences['dbkeys'] ) - - dbkeys = [ (v, k) for k, v in trans.db_builds if ( ( k in self.genomes and self.genomes[ k ].len_file ) or k in user_keys ) ] - return dbkeys - - def chroms( self, trans, dbkey=None, num=None, chrom=None, low=None ): + + def to_dict( self, num=None, chrom=None, low=None ): """ - Returns a naturally sorted list of chroms/contigs for a given dbkey. - Use either chrom or low to specify the starting chrom in the return list. + Returns representation of self as a dictionary. """ + def check_int(s): if s.isdigit(): return int(s) @@ -97,47 +62,13 @@ else: low = 0 - # If there is no dbkey owner, default to current user. - dbkey_owner, dbkey = decode_dbkey( dbkey ) - if dbkey_owner: - dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first() - else: - dbkey_user = trans.user - - # - # Get len file. - # - - # Look first in user's custom builds. - len_file = None - len_ds = None - user_keys = {} - if dbkey_user and 'dbkeys' in dbkey_user.preferences: - user_keys = from_json_string( dbkey_user.preferences['dbkeys'] ) - if dbkey in user_keys: - dbkey_attributes = user_keys[ dbkey ] - if 'fasta' in dbkey_attributes: - build_fasta = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dbkey_attributes[ 'fasta' ] ) - len_file = build_fasta.get_converted_dataset( trans, 'len' ).file_name - # Backwards compatibility: look for len file directly. - elif 'len' in dbkey_attributes: - len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ dbkey ][ 'len' ] ).file_name - - # Look in system builds. - if not len_file: - len_ds = trans.db_dataset_for( dbkey ) - if not len_ds: - len_file = self.genomes[ dbkey ].len_file - else: - len_file = len_ds.file_name - # # Get chroms data: # (a) chrom name, len; # (b) whether there are previous, next chroms; # (c) index of start chrom. # - len_file_enumerate = enumerate( open( len_file ) ) + len_file_enumerate = enumerate( open( self.len_file ) ) chroms = {} prev_chroms = False start_index = 0 @@ -169,11 +100,6 @@ start_index = low # Read chrom data from len file. - # TODO: this may be too slow for very large numbers of chroms/contigs, - # but try it out for now. - if not os.path.exists( len_file ): - return None - for line_num, line in len_file_enumerate: if line_num < low: continue @@ -197,9 +123,99 @@ to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()] to_sort.sort(lambda a,b: cmp( split_by_number(a['chrom']), split_by_number(b['chrom']) )) - return { 'reference': self.has_reference_data( trans, dbkey, dbkey_user ), 'chrom_info': to_sort, - 'prev_chroms' : prev_chroms, 'next_chroms' : next_chroms, 'start_index' : start_index } + return { + 'id': self.key, + 'reference': self.twobit_file is not None, + 'chrom_info': to_sort, + 'prev_chroms' : prev_chroms, + 'next_chroms' : next_chroms, + 'start_index' : start_index + } + +class Genomes( object ): + """ + Provides information about available genome data and methods for manipulating that data. + """ + + def __init__( self, app ): + # Create list of known genomes from len files. + self.genomes = {} + len_files = glob.glob( os.path.join( app.config.len_file_path, "*.len" ) ) + for f in len_files: + key = os.path.split( f )[1].split( ".len" )[0] + self.genomes[ key ] = Genome( key, len_file=f ) + + # Add genome data (twobit files) to genomes. + for line in open( os.path.join( app.config.tool_data_path, "twobit.loc" ) ): + if line.startswith("#"): continue + val = line.split() + if len( val ) == 2: + key, path = val + if key in self.genomes: + self.genomes[ key ].twobit_file = path + + def get_build( self, dbkey ): + """ Returns build for the given key. """ + rval = None + if dbkey in self.genomes: + rval = self.genomes[ dbkey ] + return rval + + def get_dbkeys_with_chrom_info( self, trans ): + """ Returns all valid dbkeys that have chromosome information. """ + # All user keys have a len file. + user_keys = {} + user = trans.get_user() + if 'dbkeys' in user.preferences: + user_keys = from_json_string( user.preferences['dbkeys'] ) + + dbkeys = [ (v, k) for k, v in trans.db_builds if ( ( k in self.genomes and self.genomes[ k ].len_file ) or k in user_keys ) ] + return dbkeys + + def chroms( self, trans, dbkey=None, num=None, chrom=None, low=None ): + """ + Returns a naturally sorted list of chroms/contigs for a given dbkey. + Use either chrom or low to specify the starting chrom in the return list. + """ + + # If there is no dbkey owner, default to current user. + dbkey_owner, dbkey = decode_dbkey( dbkey ) + if dbkey_owner: + dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first() + else: + dbkey_user = trans.user + + # + # Get/create genome object. + # + genome = None + + # Look first in user's custom builds. + if dbkey_user and 'dbkeys' in dbkey_user.preferences: + user_keys = from_json_string( dbkey_user.preferences['dbkeys'] ) + if dbkey in user_keys: + dbkey_attributes = user_keys[ dbkey ] + if 'fasta' in dbkey_attributes: + build_fasta = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dbkey_attributes[ 'fasta' ] ) + len_file = build_fasta.get_converted_dataset( trans, 'len' ).file_name + # Backwards compatibility: look for len file directly. + elif 'len' in dbkey_attributes: + len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ dbkey ][ 'len' ] ).file_name + if len_file: + genome = Genome( dbkey, len_file=len_file ) + + + # Look in system builds. + if not genome: + len_ds = trans.db_dataset_for( dbkey ) + if not len_ds: + genome = self.genomes[ dbkey ] + else: + gneome = Genome( dbkey, len_file=len_ds.file_name ) + + return genome.to_dict( num=num, chrom=chrom, low=low ) + def has_reference_data( self, trans, dbkey, dbkey_owner=None ): """ Returns true if there is reference data for the specified dbkey. 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