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To maintain previous behavior, list custom genome build names first.

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This commit is contained in:
Daniel Blankenberg
2014-05-20 10:18:28 -04:00
parent 49e1e48a59
commit ca7c93c729
1 changed files with 17 additions and 11 deletions
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lib/galaxy/util/dbkeys.py
+17 -11
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@@ -22,17 +22,16 @@ class GenomeBuilds( object ):
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 @@ class GenomeBuilds( object ):
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 @@ class GenomeBuilds( object ):
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 )