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Use bytestring comparisons in verify module

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This commit is contained in:
mvdbeek
2019-05-22 17:45:00 +02:00
parent ab7a38631e
commit 30bec0028d
1 changed files with 10 additions and 11 deletions
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lib/galaxy/tools/verify/__init__.py
+10 -11
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@@ -3,7 +3,6 @@
import difflib
import filecmp
import hashlib
import io
import logging
import os
import os.path
@@ -268,9 +267,9 @@ def files_diff(file1, file2, attributes=None):
def files_re_match(file1, file2, attributes=None):
"""Check the contents of 2 files for differences using re.match."""
local_file = io.open(file1, encoding='utf-8').readlines() # regex file
history_data = io.open(file2, encoding='utf-8').readlines()
assert len(local_file) == len(history_data), 'Data File and Regular Expression File contain a different number of lines (%d != %d)\nHistory Data (first 40 lines):\n%s' % (len(local_file), len(history_data), ''.join(history_data[:40]))
local_file = open(file1, 'rb').readlines() # regex file
history_data = open(file2, 'rb').readlines()
assert len(local_file) == len(history_data), b'Data File and Regular Expression File contain a different number of lines (%d != %d)\nHistory Data (first 40 lines):\n%s' % (len(local_file), len(history_data), b''.join(history_data[:40]))
if attributes is None:
attributes = {}
if attributes.get('sort', False):
@@ -279,24 +278,24 @@ def files_re_match(file1, file2, attributes=None):
line_diff_count = 0
diffs = []
for i in range(len(history_data)):
if not re.match(local_file[i].rstrip('\r\n'), history_data[i].rstrip('\r\n')):
if not re.match(local_file[i].rstrip(b'\r\n'), history_data[i].rstrip(b'\r\n')):
line_diff_count += 1
diffs.append('Regular Expression: %s\nData file : %s' % (local_file[i].rstrip('\r\n'), history_data[i].rstrip('\r\n')))
diffs.append(b'Regular Expression: %s\nData file : %s' % (local_file[i].rstrip(b'\r\n'), history_data[i].rstrip(b'\r\n')))
if line_diff_count > lines_diff:
raise AssertionError("Regular expression did not match data file (allowed variants=%i):\n%s" % (lines_diff, "".join(diffs)))
raise AssertionError(b"Regular expression did not match data file (allowed variants=%i):\n%s" % (lines_diff, b"".join(diffs)))
def files_re_match_multiline(file1, file2, attributes=None):
"""Check the contents of 2 files for differences using re.match in multiline mode."""
local_file = io.open(file1, encoding='utf-8').read() # regex file
local_file = open(file1, 'rb').read() # regex file
if attributes is None:
attributes = {}
if attributes.get('sort', False):
history_data = io.open(file2, encoding='utf-8').readlines()
history_data = open(file2, 'rb').readlines()
history_data.sort()
history_data = ''.join(history_data)
history_data = b''.join(history_data)
else:
history_data = io.open(file2, encoding='utf-8').read()
history_data = open(file2, 'rb').read()
# lines_diff not applicable to multiline matching
assert re.match(local_file, history_data, re.MULTILINE), "Multiline Regular expression did not match data file"