details:
http://www.bx.psu.edu/hg/galaxy/rev/38e533287df4
changeset: 1526:38e533287df4
user: Greg Von Kuster <greg(a)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." )