1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b3342bc20de5/ Changeset: b3342bc20de5 Branch: next-stable User: dan Date: 2014-05-20 16:01:28 Summary: Cleanup for dbkey handling. Affected #: 2 files
diff -r b29ac7cfd60ed2aaec658f520f3e47f1af4d1ab2 -r b3342bc20de522e5b98f9b97de69737b069d6d64 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -193,7 +193,7 @@
# Collect chromInfo dataset and add as parameters to incoming db_datasets = {} - ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, tool, trans=trans ) + ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, trans=trans, custom_build_hack_get_len_from_fasta_conversion=tool.id!='CONVERTER_fasta_to_len' ) if db_dataset: inp_data.update( { "chromInfo": db_dataset } ) incoming[ "chromInfo" ] = chrom_info
diff -r b29ac7cfd60ed2aaec658f520f3e47f1af4d1ab2 -r b3342bc20de522e5b98f9b97de69737b069d6d64 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -44,19 +44,18 @@ rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) return rval
- def get_chrom_info( self, dbkey, tool, trans=None ): + 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 chrom_info = None db_dataset = None # Collect chromInfo from custom builds if trans: db_dataset = trans.db_dataset_for( dbkey ) if db_dataset: - #incoming[ "chromInfo" ] = db_dataset.file_name chrom_info = db_dataset.file_name else: - # -- Get chrom_info (len file) from either a custom or built-in build. -- + # Do Custom Build handling if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): - # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ dbkey ] # HACK: the attempt to get chrom_info below will trigger the # fasta-to-len converter if the dataset is not available or, @@ -64,17 +63,19 @@ # running the fasta-to-len tool. So, use a hack in the second # condition below to avoid getting chrom_info when running the # fasta-to-len converter. - if 'fasta' in custom_build_dict and tool.id != 'CONVERTER_fasta_to_len': + if 'fasta' in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion: # Build is defined by fasta; get len file, which is obtained from converting fasta. build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] ) chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name elif 'len' in custom_build_dict: # Build is defined by len file, so use it. chrom_info = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name + # Check Data table if not chrom_info: 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 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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