From 737b5c1b197982b907badf40ad5dfa01ef78cb96 Mon Sep 17 00:00:00 2001
From: JensWendt <92271654+JensWendt@users.noreply.github.com>
Date: Tue, 2 Jun 2026 12:44:20 +0200
Subject: [PATCH 1/2] Added UTF-8 encoding to writers for cross-OS
 compatibility

---
 src/generate_xml.py       | 6 +++---
 src/omero_cli_transfer.py | 4 ++--
 tmp_encoding_probe.xml    | 2 ++
 3 files changed, 7 insertions(+), 5 deletions(-)
 create mode 100644 tmp_encoding_probe.xml

diff --git a/src/generate_xml.py b/src/generate_xml.py
index 748f574..efc09c8 100644
--- a/src/generate_xml.py
+++ b/src/generate_xml.py
@@ -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)
@@ -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)
@@ -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
diff --git a/src/omero_cli_transfer.py b/src/omero_cli_transfer.py
index 7b7505f..5a925ba 100644
--- a/src/omero_cli_transfer.py
+++ b/src/omero_cli_transfer.py
@@ -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
@@ -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":
diff --git a/tmp_encoding_probe.xml b/tmp_encoding_probe.xml
new file mode 100644
index 0000000..cb44048
--- /dev/null
+++ b/tmp_encoding_probe.xml
@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<root>ü</root>
\ No newline at end of file

From abf57c42ca7182471e3a8b0fdb96ada4a19c8fec Mon Sep 17 00:00:00 2001
From: JensWendt <92271654+JensWendt@users.noreply.github.com>
Date: Tue, 2 Jun 2026 12:55:08 +0200
Subject: [PATCH 2/2] removed tmp file

---
 tmp_encoding_probe.xml | 2 --
 1 file changed, 2 deletions(-)
 delete mode 100644 tmp_encoding_probe.xml

diff --git a/tmp_encoding_probe.xml b/tmp_encoding_probe.xml
deleted file mode 100644
index cb44048..0000000
--- a/tmp_encoding_probe.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<root>ü</root>
\ No newline at end of file