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Merged in dan/galaxy-central-prs/stable (pull request #666)

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[STABLE] Several Fixes for Tool Data Tables
This commit is contained in:
John Chilton
2015-02-11 12:54:36 -05:00
parent 2fbb3d67d2 41fcc8ecdb
commit c9f6926a86
1 changed files with 6 additions and 3 deletions
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lib/galaxy/tools/data/__init__.py
+6 -3
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@@ -335,11 +335,13 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
def get_named_fields_list( self ):
rval = []
named_colums = self.get_column_name_list()
named_columns = self.get_column_name_list()
for fields in self.get_fields():
field_dict = {}
for i, field in enumerate( fields ):
field_name = named_colums[i]
if i == len( named_columns ):
break
field_name = named_columns[i]
if field_name is None:
field_name = i #check that this is supposed to be 0 based.
field_dict[ field_name ] = field
@@ -366,6 +368,7 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
self.columns[ name ] = index
self.largest_index = index
else:
self.largest_index = 0
for column_elem in config_element.findall( 'column' ):
name = column_elem.get( 'name', None )
assert name is not None, "Required 'name' attribute missing from column def"
@@ -495,7 +498,7 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
try:
data_table_fh = open( filename, 'r+b' )
except IOError, e:
log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', self.filename, e )
log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', filename, e )
data_table_fh = open( filename, 'wb' )
if os.stat( filename )[6] != 0:
# ensure last existing line ends with new line