diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index d3505088219..87e29c3239f 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -51,9 +51,8 @@
-
-
-
+
+
@@ -494,7 +493,8 @@
-
+
+
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 2456557cf88..92d6e833e10 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -946,7 +946,7 @@ class CSV( TabularData ):
@dataproviders.decorators.has_dataproviders
-class Base_CSV( CSV ):
+class BaseCSV( CSV ):
"""
Delimiter-separated table data.
This includes CSV, TSV and other dialects understood by the
@@ -954,42 +954,37 @@ class Base_CSV( CSV ):
Must be extended to define the dialect to use, strict_width: and file_ext.
See Python module csv for documentation of dialect settings
"""
- #dialect Set by subclass
- #file_ext Set by subclass
- #strict_width Set by subclass
- #If set sniff fails is a single row is incorrect.
- #Python's csv is more tollerant
big_peek_size = 10240 # Large File chunk used for sniffing CSV dialect
def sniff( self, filename ):
""" Return True if if recognizes dialect and header. """
try:
- #check the dialect works
+ # check the dialect works
reader = csv.reader(open(filename, 'r'), self.dialect)
- #Check we can read header and get columns
+ # Check we can read header and get columns
header_row = reader.next()
if len(header_row) < 2:
- #No columns so not seperated by this dialect.
+ # No columns so not seperated by this dialect.
return False
- #check all rows can be read as otherwise set_meta throws an exception
+ # check all rows can be read as otherwise set_meta throws an exception
if self.strict_width:
num_columns = len(header_row)
for data_row in reader:
- #All columns must be the same length
+ # All columns must be the same length
if num_columns != len(data_row):
return False
else:
- #Check the next row as it is used by set_meta
+ # Check the next row as it is used by set_meta
data_row = reader.next()
if len(data_row) < 2:
- #No columns so not seperated by this dialect.
+ # No columns so not seperated by this dialect.
return False
- #ignore the length in the rest
+ # ignore the length in the rest
for data_row in reader:
pass
- #Optional: Check Python's csv comes up with a similar dialect
+ # Optional: Check Python's csv comes up with a similar dialect
auto_dialect = csv.Sniffer().sniff(open(filename, 'r').read(self.big_peek_size))
if (auto_dialect.delimiter != self.dialect.delimiter):
return False
@@ -1010,7 +1005,7 @@ class Base_CSV( CSV ):
return True
except:
- #Not readable by Python's csv using this dialect
+ # Not readable by Python's csv using this dialect
return False
def set_meta( self, dataset, **kwd ):
@@ -1042,25 +1037,21 @@ class Base_CSV( CSV ):
@dataproviders.decorators.has_dataproviders
-class Excell_CSV( Base_CSV ):
+class ExcelCSV( BaseCSV ):
"""
Comma separated table data.
Only sniffs comma seperated files with at least 2 columns
"""
def __init__(self, **kwd):
- Base_CSV.__init__( self, **kwd )
+ BaseCSV.__init__( self, **kwd )
self.dialect = csv.excel # This is the default
- #delimiter = ','
- #quotechar = '"'
- #doublequote = True
- #skipinitialspace = False
self.file_ext = 'csv' # File extension
self.strict_width = False # Previous csv type did not check column width
@dataproviders.decorators.has_dataproviders
-class Excell_TSV( Base_CSV ):
+class ExcelTSV( BaseCSV ):
"""
Comma separated table data.
Only sniff tab seperated files with at least two columns
@@ -1073,12 +1064,8 @@ class Excell_TSV( Base_CSV ):
"""
def __init__(self, **kwd):
- Base_CSV.__init__( self, **kwd )
+ BaseCSV.__init__( self, **kwd )
self.dialect = csv.excel_tab
- #delimiter = '\t'
- #quotechar = '"'
- #doublequote = True
- #skipinitialspace = False
self.file_ext = 'tsv' # File extension
self.strict_width = True # Leave files with different width to tabular