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Added UTF-8 encoding to writers for cross-OS compatibility #119

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Merged
erickmartins merged 2 commits into from
Jun 5, 2026
+5 −5
Merged

Added UTF-8 encoding to writers for cross-OS compatibility #119

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737b5c1
Added UTF-8 encoding to writers for cross-OS compatibility
JensWendt Jun 2, 2026
abf57c4
removed tmp file
JensWendt Jun 2, 2026
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6 changes: 3 additions & 3 deletions src/generate_xml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -989,7 +989,7 @@ def populate_xml(datatype: str, id: int, filepath: str, conn: BlitzGateway,
if (not (barchive or simple)) and figure:
populate_figures(ome, conn, filepath)
if not barchive:
with open(filepath, 'w') as fp:
with open(filepath, 'w', encoding='utf-8') as fp:
print(to_xml(ome), file=fp)
fp.close()
path_id_dict = list_file_ids(ome)
Expand All @@ -1009,7 +1009,7 @@ def populate_xml_folder(folder: str, filelist: bool) -> Tuple[OME, dict]:
filepath = str(Path(folder) / "transfer.xml")
else:
raise ValueError("Folder cannot be found!")
with open(filepath, 'w') as fp:
with open(filepath, 'w', encoding='utf-8') as fp:
print(to_xml(ome), file=fp)
fp.close()
path_id_dict = list_file_ids(ome)
Expand All @@ -1022,7 +1022,7 @@ def populate_tsv(datatype: str, ome: OME, filepath: str,
logger.warning("Bioimage Archive export of Plate/Screen"
" currently unsupported")
return
with open(filepath, 'w') as fp:
with open(filepath, 'w', encoding='utf-8', newline='') as fp:
write_lines(datatype, ome, fp, path_id_dict, folder)
fp.close()
return
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4 changes: 2 additions & 2 deletions src/omero_cli_transfer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -479,7 +479,7 @@ def _fix_pixels_image_simple(self, ome: OME, folder: str, filepath: str
os.path.join(str(Path(folder)), path2))
if os.path.exists(os.path.join(str(Path(folder)), "pixel_images")):
shutil.rmtree(os.path.join(str(Path(folder)), "pixel_images"))
with open(filepath, 'w') as fp:
with open(filepath, 'w', encoding='utf-8') as fp:
print(to_xml(newome), file=fp)
fp.close()
return newome
Expand Down Expand Up @@ -563,7 +563,7 @@ def __pack(self, args):
path_id_dict.update(this_id_dict)
# need to somehow merge omes/path_id_dicts
if not args.barchive:
with open(md_fp, 'w') as fp:
with open(md_fp, 'w', encoding='utf-8') as fp:
print(to_xml(ome), file=fp)
fp.close()
if args.binaries == "all":
Expand Down
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