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:
chrom_info = db_dataset.file_name
else:
# Do Custom Build handling
if trans.user and ('dbkeys' in trans.user.preferences) and (
dbkey in loads(trans.user.preferences['dbkeys'])):
custom_build_dict = loads(
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,
# which will in turn create a recursive loop when
# 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 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 server len path
if not chrom_info:
# Default to built-in build.
# Since we are using an unverified dbkey, we will sanitize the dbkey before use
chrom_info = os.path.join(
self._static_chrom_info_path,
"%s.len" % sanitize_lists_to_string(dbkey))
chrom_info = os.path.abspath(chrom_info)
return (chrom_info, db_dataset)
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:
chrom_info = db_dataset.file_name
else:
# Do Custom Build handling
if trans.user and ('dbkeys' in trans.user.preferences) and (dbkey in loads(trans.user.preferences['dbkeys'])):
custom_build_dict = loads(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,
# which will in turn create a recursive loop when
# 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 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 server len path
if not chrom_info:
# Default to built-in build.
# Since we are using an unverified dbkey, we will sanitize the dbkey before use
chrom_info = os.path.join(self._static_chrom_info_path, "%s.len" % sanitize_lists_to_string(dbkey))
chrom_info = os.path.abspath(chrom_info)
return (chrom_info, db_dataset)
def to_safe_string(self, value):
return sanitize_lists_to_string(self.to_string(value))
def to_safe_string( self, value ):
return sanitize_lists_to_string( self.to_string( value ) )
