details: http://www.bx.psu.edu/hg/galaxy/rev/38e533287df4 changeset: 1526:38e533287df4 user: Greg Von Kuster greg@bx.psu.edu date: Wed Sep 24 11:14:44 2008 -0400 description: Convert metadata unicode strings to ascii ( previous code doesn't seem to do anything, am I missing something? ). Add no_value metadata attribute to columns and column_types metadata. Fix for column_maker and filter tools.
4 file(s) affected in this change:
lib/galaxy/datatypes/metadata.py lib/galaxy/datatypes/tabular.py tools/stats/column_maker.py tools/stats/filtering.py
diffs (79 lines):
diff -r 675ad84ae008 -r 38e533287df4 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Mon Sep 22 12:02:35 2008 -0400 +++ b/lib/galaxy/datatypes/metadata.py Wed Sep 24 11:14:44 2008 -0400 @@ -60,10 +60,10 @@ if isinstance( value, ListType ): for i, elem in enumerate( value ): if type ( elem ) == unicode: - value[i] = str( elem ) + value[i] = elem.decode( 'ascii' ) elif isinstance ( value, basestring ): if type( value ) == unicode: - value = str( value ) + value = value.decode( 'ascii' ) self.value = value self.context = context self.display = True @@ -76,7 +76,7 @@ @classmethod def marshal( cls, value ): ''' - This method should/can be overridden to convert the incomming + This method should/can be overridden to convert the incoming value to whatever type it is supposed to be. ''' return value @@ -273,7 +273,6 @@ class ColumnTypesParameter( MetadataParameter ): def __init__( self, spec, value, context ): MetadataParameter.__init__( self, spec, value, context ) - def __str__(self): return ",".join( map( str, self.value ) )
diff -r 675ad84ae008 -r 38e533287df4 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Mon Sep 22 12:02:35 2008 -0400 +++ b/lib/galaxy/datatypes/tabular.py Wed Sep 24 11:14:44 2008 -0400 @@ -19,8 +19,8 @@ """Tab delimited data"""
"""Add metadata elements""" - MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False ) - MetadataElement( name="column_types", default=[], desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False ) + MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False, no_value=0 ) + MetadataElement( name="column_types", default=[], desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[] )
def init_meta( self, dataset, copy_from=None ): data.Text.init_meta( self, dataset, copy_from=copy_from ) diff -r 675ad84ae008 -r 38e533287df4 tools/stats/column_maker.py --- a/tools/stats/column_maker.py Mon Sep 22 12:02:35 2008 -0400 +++ b/tools/stats/column_maker.py Wed Sep 24 11:14:44 2008 -0400 @@ -19,12 +19,10 @@ round = sys.argv[4] try: in_columns = int( sys.argv[5] ) - # in_column_types is passed as a string that looks something like: - # "[u'str', u'int', u'int', u'str', u'int', u'str']" - in_column_types = sys.argv[6].strip( '[' ).strip( ']' ).replace( 'u', '' ).replace( "'", '' ).split( ',' ) + in_column_types = sys.argv[6].split( ',' ) except: stop_err( "Data does not appear to be tabular. This tool can only be used with tab-delimited data." ) - + # Unescape if input has been escaped mapped_str = { '__lt__': '<', diff -r 675ad84ae008 -r 38e533287df4 tools/stats/filtering.py --- a/tools/stats/filtering.py Mon Sep 22 12:02:35 2008 -0400 +++ b/tools/stats/filtering.py Wed Sep 24 11:14:44 2008 -0400 @@ -26,9 +26,7 @@ cond_text = sys.argv[3] try: in_columns = int( sys.argv[4] ) - # in_column_types is passed as a string that looks something like: - # "[u'str', u'int', u'int', u'str', u'int', u'str']" - in_column_types = sys.argv[5].strip( '[' ).strip( ']' ).replace( 'u', '' ).replace( "'", '' ).split( ',' ) + in_column_types = sys.argv[5].split( ',' ) except: stop_err( "Data does not appear to be tabular. This tool can only be used with tab-delimited data." )