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Fix newline conversion on python 3 if no encoding is set

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This commit is contained in:
mvdbeek
2018-10-30 09:27:25 +01:00
parent 09601ad4ef
commit d168042b36
1 changed files with 14 additions and 13 deletions
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lib/galaxy/datatypes/sniff.py
+14 -13
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@@ -5,6 +5,7 @@ from __future__ import absolute_import
import codecs
import gzip
import io
import logging
import os
import re
@@ -116,9 +117,9 @@ def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload"):
'1 2\\n3 4\\n'
"""
fd, temp_name = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir)
with os.fdopen(fd, "wt") as fp:
with io.open(fd, mode="wt", encoding='utf-8') as fp:
i = None
for i, line in enumerate(open(fname, "U")):
for i, line in enumerate(io.open(fname, mode="U", encoding='utf-8')):
fp.write("%s\n" % line.rstrip("\r\n"))
if i is None:
i = 0
@@ -132,13 +133,13 @@ def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload"):
return (i, temp_name)
def sep2tabs(fname, in_place=True, patt="\\s+", tmp_dir=None, tmp_prefix="gxupload"):
def sep2tabs(fname, in_place=True, patt=r"\s+", tmp_dir=None, tmp_prefix="gxupload"):
"""
Transforms in place a 'sep' separated file to a tab separated one
>>> fname = get_test_fname('temp.txt')
>>> with open(fname, 'wt') as fh:
... _ = fh.write("1 2\\n3 4\\n")
... _ = fh.write(u"1 2\\n3 4\\n")
>>> sep2tabs(fname)
(2, None)
>>> open(fname).read()
@@ -146,17 +147,17 @@ def sep2tabs(fname, in_place=True, patt="\\s+", tmp_dir=None, tmp_prefix="gxuplo
"""
regexp = re.compile(patt)
fd, temp_name = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir)
with os.fdopen(fd, "wt") as fp:
with io.open(fd, mode="wt", encoding='utf-8') as fp:
i = None
for i, line in enumerate(open(fname)):
for i, line in enumerate(io.open(fname, encoding='utf-8')):
if line.endswith("\r"):
line = line.rstrip('\r')
elems = regexp.split(line)
fp.write("%s\r" % '\t'.join(elems))
fp.write(u"%s\r" % '\t'.join(elems))
else:
line = line.rstrip('\n')
elems = regexp.split(line)
fp.write("%s\n" % '\t'.join(elems))
fp.write(u"%s\n" % '\t'.join(elems))
if i is None:
i = 0
else:
@@ -169,14 +170,14 @@ def sep2tabs(fname, in_place=True, patt="\\s+", tmp_dir=None, tmp_prefix="gxuplo
return (i, temp_name)
def convert_newlines_sep2tabs(fname, in_place=True, patt="\\s+", tmp_dir=None, tmp_prefix="gxupload"):
def convert_newlines_sep2tabs(fname, in_place=True, patt="\s+", tmp_dir=None, tmp_prefix="gxupload"):
"""
Combines above methods: convert_newlines() and sep2tabs()
so that files do not need to be read twice
>>> fname = get_test_fname('temp.txt')
>>> with open(fname, 'wt') as fh:
... _ = fh.write("1 2\\r3 4")
... _ = fh.write(u"1 2\\r3 4")
>>> convert_newlines_sep2tabs(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir())
(2, None)
>>> open(fname).read()
@@ -184,11 +185,11 @@ def convert_newlines_sep2tabs(fname, in_place=True, patt="\\s+", tmp_dir=None, t
"""
regexp = re.compile(patt)
fd, temp_name = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir)
with os.fdopen(fd, "wt") as fp:
for i, line in enumerate(open(fname, "U")):
with io.open(fd, mode="wt", encoding='utf-8') as fp:
for i, line in enumerate(codecs.open(fname, mode="U", encoding='utf-8')):
line = line.rstrip('\r\n')
elems = regexp.split(line)
fp.write("%s\n" % '\t'.join(elems))
fp.write(u"%s\n" % '\t'.join(elems))
if in_place:
shutil.move(temp_name, fname)
# Return number of lines in file.