From 63825a478406f167e5416d61d573ee67adf5f2ea Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 21 Oct 2014 16:30:59 +0200
Subject: [PATCH] Handle encoding for command line file arguments
---
mutalyzer/entrypoints/__init__.py | 5 ++++-
mutalyzer/entrypoints/admin.py | 26 +++++++++++++++++++++-----
mutalyzer/mapping.py | 1 -
3 files changed, 25 insertions(+), 7 deletions(-)
diff --git a/mutalyzer/entrypoints/__init__.py b/mutalyzer/entrypoints/__init__.py
index 5c6d2cf6..7d95d01e 100644
--- a/mutalyzer/entrypoints/__init__.py
+++ b/mutalyzer/entrypoints/__init__.py
@@ -5,6 +5,7 @@ Entry points to Mutalyzer.
from __future__ import unicode_literals
+import locale
import sys
@@ -48,6 +49,8 @@ def _cli_string(argument):
Decode a command line argument byte string to unicode using our best
guess for the encoding (noop on unicode strings).
"""
+ encoding = sys.stdin.encoding or locale.getpreferredencoding()
+
if isinstance(argument, unicode):
return argument
- return unicode(argument, encoding=sys.stdin.encoding)
+ return unicode(argument, encoding=encoding)
diff --git a/mutalyzer/entrypoints/admin.py b/mutalyzer/entrypoints/admin.py
index 9b06920d..e7c74178 100644
--- a/mutalyzer/entrypoints/admin.py
+++ b/mutalyzer/entrypoints/admin.py
@@ -6,9 +6,10 @@ Command line interface to Mutalyzer administrative tools.
from __future__ import unicode_literals
import argparse
+import codecs
import json
+import locale
import os
-import sys
import alembic.command
import alembic.config
@@ -29,10 +30,12 @@ class UserError(Exception):
pass
-def add_assembly(assembly_file):
+def add_assembly(assembly_file, encoding):
"""
Add genome assembly definition from a JSON file.
"""
+ assembly_file = codecs.getreader(encoding)(assembly_file)
+
try:
definition = json.load(assembly_file)
except ValueError:
@@ -87,10 +90,13 @@ def list_assemblies():
assembly.taxonomy_id)
-def import_mapview(assembly_name_or_alias, mapview_file, group_label):
+def import_mapview(assembly_name_or_alias, mapview_file, encoding,
+ group_label):
"""
Import transcript mappings from an NCBI mapview file.
"""
+ mapview_file = codecs.getreader(encoding)(mapview_file)
+
try:
assembly = Assembly.by_name_or_alias(assembly_name_or_alias)
except NoResultFound:
@@ -185,6 +191,8 @@ def main():
"""
Command-line interface to Mutalyzer administrative tools.
"""
+ default_encoding = locale.getpreferredencoding()
+
assembly_parser = argparse.ArgumentParser(add_help=False)
assembly_parser.add_argument(
'-a', '--assembly', metavar='ASSEMBLY', type=_cli_string,
@@ -214,9 +222,13 @@ def main():
description=add_assembly.__doc__.split('\n\n')[0])
p.set_defaults(func=add_assembly)
p.add_argument(
- 'assembly_file', metavar='FILE', type=argparse.FileType('r'),
+ 'assembly_file', metavar='FILE', type=argparse.FileType('rb'),
help='genome assembly definition JSON file (example: '
'extras/assemblies/GRCh37.json)')
+ p.add_argument(
+ '--encoding', metavar='ENCODING', type=_cli_string,
+ default=default_encoding,
+ help='input file encoding (default: %s)' % default_encoding)
# Subparser 'assemblies import-mapview'.
p = s.add_parser(
@@ -228,8 +240,12 @@ def main():
'`sort -t $\'\\t\' -k 11,11 -k 2,2` command.')
p.set_defaults(func=import_mapview)
p.add_argument(
- 'mapview_file', metavar='FILE', type=argparse.FileType('r'),
+ 'mapview_file', metavar='FILE', type=argparse.FileType('rb'),
help='file from NCBI mapview (example: seq_gene.md), see note below')
+ p.add_argument(
+ '--encoding', metavar='ENCODING', type=_cli_string,
+ default=default_encoding,
+ help='input file encoding (default: %s)' % default_encoding)
p.add_argument(
'group_label', metavar='GROUP_LABEL', type=_cli_string,
help='use only entries with this group label (example: '
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index e5bd96db..11e05899 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -883,7 +883,6 @@ def import_from_reference(assembly, reference):
session.commit()
-# Todo: File must be opened with the correct encoding.
def import_from_mapview_file(assembly, mapview_file, group_label):
"""
Import transcript mappings from an NCBI mapview file.
--
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