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Custom build bug fix to indicate availability of reference data during conversion. Parameter cleanup via Pylint as well.

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This commit is contained in:
Jeremy Goecks
2013-04-09 16:48:08 -04:00
parent be0a279497
commit e2e4448c3c
1 changed files with 9 additions and 5 deletions
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lib/galaxy/visualization/genomes.py
+9 -5
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@@ -242,12 +242,16 @@ class Genomes( object ):
if dbkey in user_keys:
dbkey_attributes = user_keys[ dbkey ]
dbkey_name = dbkey_attributes[ 'name' ]
# If there's a fasta for genome, convert to 2bit for later use.
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
converted_dataset = build_fasta.get_converted_dataset( trans, 'twobit' )
if converted_dataset:
twobit_file = converted_dataset.file_name
build_fasta.get_converted_dataset( trans, 'twobit' )
# HACK: set twobit_file to True rather than a file name because
# get_converted_dataset returns null during conversion even though
# there will eventually be a twobit file available for genome.
twobit_file = True
# 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
@@ -275,7 +279,7 @@ class Genomes( object ):
return rval
def has_reference_data( self, trans, dbkey, dbkey_owner=None ):
def has_reference_data( self, dbkey, dbkey_owner=None ):
"""
Returns true if there is reference data for the specified dbkey. If dbkey is custom,
dbkey_owner is needed to determine if there is reference data.
@@ -308,7 +312,7 @@ class Genomes( object ):
else:
dbkey_user = trans.user
if not self.has_reference_data( trans, dbkey, dbkey_user ):
if not self.has_reference_data( dbkey, dbkey_user ):
return None
#