From 361625a12c7cfc126223f7f4c4b12756d8d4ecfa Mon Sep 17 00:00:00 2001
From: Robert Izzard <r.izzard@surrey.ac.uk>
Date: Sun, 28 Nov 2021 11:39:31 +0000
Subject: [PATCH] force file.open to use textmode unless binary is specified
---
binarycpython/utils/dataIO.py | 26 ++++++++++++++++++++------
binarycpython/utils/grid.py | 7 ++++++-
2 files changed, 26 insertions(+), 7 deletions(-)
diff --git a/binarycpython/utils/dataIO.py b/binarycpython/utils/dataIO.py
index 1bcf59a7a..f6e8990bc 100644
--- a/binarycpython/utils/dataIO.py
+++ b/binarycpython/utils/dataIO.py
@@ -634,8 +634,7 @@ class dataIO():
# error on open should be fatal
except Exception as e:
- if vb:
- print("Error in locked_open_for_write() : {}".format(e))
+ print("Error in locked_open_for_write() : {}".format(e))
if fatal_open_errors:
if vb:
print("fatal exit on open")
@@ -677,25 +676,40 @@ class dataIO():
"""
Wrapper for open() with automatic compression based on the file extension.
"""
+
if compression is None:
compression = self.compression_type(file)
+ print("open() with mode = {mode}, compression {compression}".format(
+ compression=compression,
+ mode=mode))
if compression:
if compresslevel is None:
compresslevel = 9
+ if not 'b' in mode:
+ # if we don't specify binary-mode, the gzip module
+ # defaults to binary, which isn't compatible with JSON,
+ # so default to text if not specified otherwise
+ mode += 't'
+ else:
+ encoding = None
+ errors = None
+ newline = None
if compression is "bzip2":
file_object = bz2.open(file,
mode=mode,
compresslevel=compresslevel,
encoding=encoding,
- error=errors,
- newline=newline)
+ errors=errors,
+ newline=newline
+ )
elif compression is "gzip":
file_object = gzip.open(file,
mode=mode,
compresslevel=compresslevel,
encoding=encoding,
- error=errors,
- newline=newline)
+ errors=errors,
+ newline=newline
+ )
else:
file_object = open(file,
mode=mode,
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
index 4b1ec7011..39441f43b 100644
--- a/binarycpython/utils/grid.py
+++ b/binarycpython/utils/grid.py
@@ -622,8 +622,11 @@ class Population(analytics,
settings_name
)
+ print("ok")
+
# open locked settings file, then output if we get the lock
- (f,lock) = self.locked_open_for_write(settings_fullname)
+ (f,lock) = self.locked_open_for_write(settings_fullname,vb=True)
+ print("ok")
if lock and f:
self.verbose_print(
@@ -638,7 +641,9 @@ class Population(analytics,
default=binaryc_json_serializer,
ensure_ascii=ensure_ascii
)
+ print("ok pre")
self.locked_close(f,lock)
+ print("ok ret")
return settings_fullname
else:
msg = "Exporting all info without passing a value for `outfile` requires custom_options['data_dir'] to be present. That is not the cause. Either set the `data_dir` or pass a value for `outfile` "
--
GitLab