1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f3948f90b900/ Changeset: f3948f90b900 Branch: next-stable User: dan Date: 2014-05-20 16:18:28 Summary: To maintain previous behavior, list custom genome build names first. Affected #: 1 file
diff -r b3342bc20de522e5b98f9b97de69737b069d6d64 -r f3948f90b9002ae47f0941b0e39cb63d122415a3 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -22,17 +22,16 @@ self._static_dbkeys[ key ] = value
def get_genome_build_names( self, trans=None ): - #FIXME: how to deal with key duplicates? - #Load old builds.txt static keys - rval = ( self._static_dbkeys.items() ) - #load dbkeys from dbkey data table - dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) - if dbkey_table is not None: - for field_dict in dbkey_table.get_named_fields_list(): - rval.append( ( field_dict[ 'value' ], field_dict[ 'name' ] ) ) - #load user custom genome builds + # FIXME: how to deal with key duplicates? + rval = [] + # load user custom genome builds if trans is not None: if trans.history: + # This is a little bit Odd. We are adding every .len file in the current history to dbkey list, + # but this is previous behavior from trans.db_names, so we'll continue to do it. + # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering, + # so a len file will be listed twice (as the build name and again as dataset name), + # if custom dbkey creation/conversion occurred within the current history. datasets = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=trans.history.id, extension="len" ) for dataset in datasets: @@ -42,10 +41,17 @@ user_keys = from_json_string( user.preferences['dbkeys'] ) for key, chrom_dict in user_keys.iteritems(): rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) + # Load old builds.txt static keys + rval.extend( self._static_dbkeys.items() ) + #load dbkeys from dbkey data table + dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) + if dbkey_table is not None: + for field_dict in dbkey_table.get_named_fields_list(): + rval.append( ( field_dict[ 'value' ], field_dict[ 'name' ] ) ) return rval
def get_chrom_info( self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True ): - #FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required + # FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required chrom_info = None db_dataset = None # Collect chromInfo from custom builds @@ -75,7 +81,7 @@ dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) if dbkey_table is not None: chrom_info = dbkey_table.get_entry( 'value', dbkey, 'len_path', default=None ) - #use configured len path + # use configured server len path if not chrom_info: # Default to built-in build. chrom_info = os.path.join( self._static_chrom_info_path, "%s.len" % dbkey )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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