Add OSError_from_errno() utility function

jmarshall · jmarshall · commit bc19635b79d0 · 2025-05-29T21:03:00.000+12:00
diff --git a/pysam/libcutils.pxd b/pysam/libcutils.pxd
@@ -9,6 +9,8 @@ cpdef parse_region(contig=*, start=*, stop=*, region=*, reference=*, end=*)
 
 cdef int libc_whence_from_io(int whence)
 
+cdef OSError_from_errno(message, filename=*)
+
 #########################################################################
 # Utility functions for quality string conversions
 
diff --git a/pysam/libcutils.pyx b/pysam/libcutils.pyx
@@ -14,7 +14,7 @@ from cpython cimport PyBytes_Check, PyUnicode_Check
 from cpython cimport array as c_array
 from libc.errno cimport errno
 from libc.stdlib cimport calloc, free
-from libc.string cimport strncpy
+from libc.string cimport strerror, strncpy
 from libc.stdint cimport INT32_MAX, int32_t
 from libc.stdio cimport fprintf, stderr, fflush
 from libc.stdio cimport stdout as c_stdout
@@ -175,6 +175,12 @@ cdef decode_bytes(bytes s, encoding=None, errors=None):
         return s.decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
 
 
+cdef OSError_from_errno(message, filename=None):
+    cdef int err = errno
+    if filename is not None: filename = os.fsdecode(filename)
+    return OSError(err, f"{message}: {strerror(err).decode()}", filename)
+
+
 cpdef parse_region(contig=None,
                    start=None,
                    stop=None,
@@ -324,7 +330,7 @@ def _pysam_dispatch(collection,
         stdout_h = c_open(force_bytes(stdout_f),
                           O_WRONLY|O_CREAT|O_TRUNC, 0666)
         if stdout_h == -1:
-            raise OSError(errno, "error while opening file for writing", stdout_f)
+            raise OSError_from_errno("Could not redirect standard output", stdout_f)
 
         samtools_set_stdout_fn(force_bytes(stdout_f))
         bcftools_set_stdout_fn(force_bytes(stdout_f))
