From e55dddd92fa9c2dcd7b021181fb7a73552b88f79 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 24 Nov 2023 09:16:12 +0100
Subject: [PATCH] Fix append mode bug

---
 CHANGELOG.rst                |  5 +++++
 src/isal/igzip_threaded.py   |  8 +++++++-
 tests/test_igzip_threaded.py | 22 ++++++++++++++++++++++
 3 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 3e936f62..de602380 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -7,6 +7,11 @@ Changelog
 .. This document is user facing. Please word the changes in such a way
 .. that users understand how the changes affect the new version.
 
+version 1.5.3
+-----------------
++ Fix a bug where append mode would not work when using
+  ``igzip_threaded.open``.
+
 version 1.5.2
 -----------------
 + Fix a bug where a filehandle remained opened when ``igzip_threaded.open``
diff --git a/src/isal/igzip_threaded.py b/src/isal/igzip_threaded.py
index dd34e704..99eafc17 100644
--- a/src/isal/igzip_threaded.py
+++ b/src/isal/igzip_threaded.py
@@ -63,6 +63,7 @@ def open(filename, mode="rb", compresslevel=igzip._COMPRESS_LEVEL_TRADEOFF,
         gzip_file = io.BufferedWriter(
             _ThreadedGzipWriter(
                 filename,
+                mode.replace("t", "b"),
                 block_size=block_size,
                 level=compresslevel,
                 threads=threads
@@ -197,11 +198,16 @@ class _ThreadedGzipWriter(io.RawIOBase):
     """
     def __init__(self,
                  filename,
+                 mode: str = "wb",
                  level: int = isal_zlib.ISAL_DEFAULT_COMPRESSION,
                  threads: int = 1,
                  queue_size: int = 1,
                  block_size: int = 1024 * 1024,
                  ):
+        if "t" in mode or "r" in mode:
+            raise ValueError("Only binary writing is supported")
+        if "b" not in mode:
+            mode += "b"
         self.lock = threading.Lock()
         self.exception: Optional[Exception] = None
         self.level = level
@@ -238,7 +244,7 @@ def __init__(self,
         self.running = False
         self._size = 0
         self._closed = False
-        self.raw = open_as_binary_stream(filename, "wb")
+        self.raw = open_as_binary_stream(filename, mode)
         self._write_gzip_header()
         self.start()
 
diff --git a/tests/test_igzip_threaded.py b/tests/test_igzip_threaded.py
index be6c3ca4..dbee85f8 100644
--- a/tests/test_igzip_threaded.py
+++ b/tests/test_igzip_threaded.py
@@ -169,3 +169,25 @@ def test_writer_write_after_close(threads):
     with pytest.raises(ValueError) as error:
         f.write(b"abc")
     error.match("closed")
+
+
+def test_igzip_threaded_append(tmp_path):
+    test_file = tmp_path / "test.txt.gz"
+    with igzip_threaded.open(test_file, "wb") as f:
+        f.write(b"AB")
+    with igzip_threaded.open(test_file, mode="ab") as f:
+        f.write(b"CD")
+    with gzip.open(test_file, "rb") as f:
+        contents = f.read()
+    assert contents == b"ABCD"
+
+
+def test_igzip_threaded_append_text_mode(tmp_path):
+    test_file = tmp_path / "test.txt.gz"
+    with igzip_threaded.open(test_file, "wt") as f:
+        f.write("AB")
+    with igzip_threaded.open(test_file, mode="at") as f:
+        f.write("CD")
+    with gzip.open(test_file, "rt") as f:
+        contents = f.read()
+    assert contents == "ABCD"