From 08132b29a68de73694353fe1c503e1bbe8556bc5 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 19 Jan 2024 17:05:28 +0100
Subject: [PATCH] Refactor init function for PipedCompressionProgram

---
 src/xopen/__init__.py | 74 +++++++++++++++++++------------------------
 1 file changed, 33 insertions(+), 41 deletions(-)

diff --git a/src/xopen/__init__.py b/src/xopen/__init__.py
index ce56f08..12cc4ed 100644
--- a/src/xopen/__init__.py
+++ b/src/xopen/__init__.py
@@ -190,6 +190,7 @@ def __init__(
             used. At the moment, this means that the number of available CPU cores is used, capped
             at four to avoid creating too many threads. Use 0 to use all available cores.
         """
+        self._program_args = program_args[:]
         if mode not in ("r", "rb", "w", "wb", "a", "ab"):
             raise ValueError(
                 "Mode is '{}', but it must be 'r', 'rb', 'w', 'wb', 'a', or 'ab'".format(
@@ -200,10 +201,8 @@ def __init__(
         if isinstance(path, bytes) and sys.platform == "win32":
             path = path.decode()
         self.name: str = str(path)
-        self._path = path
         self._mode: str = mode
         self._stderr = tempfile.TemporaryFile("w+b")
-        self._program_args: List[str] = program_args
         self._threads_flag: Optional[str] = threads_flag
 
         if threads is None:
@@ -214,23 +213,45 @@ def __init__(
             else:
                 threads = min(_available_cpu_count(), 4)
         self._threads = threads
-        if "r" not in mode:
-            self.outfile: Optional[BinaryIO] = open(path, mode[0] + "b")
-        else:
-            self.outfile = None
-        try:
-            self.process = self._open_process(mode, compresslevel, threads)
-        except OSError:
-            if self.outfile:
-                self.outfile.close()
-            raise
+
+        if threads != 0 and self._threads_flag is not None:
+            self._program_args += [f"{self._threads_flag}{threads}"]
+
+        # Setting close_fds to True in the Popen arguments is necessary due to
+        # <http://bugs.python.org/issue12786>.
+        # However, close_fds is not supported on Windows. See
+        # <https://github.com/marcelm/cutadapt/issues/315>.
+        kwargs = {}
+        if sys.platform != "win32":
+            kwargs["close_fds"] = True
+
         if "r" in mode:
+            self._program_args += ["-c", "-d", path]  # type: ignore
+            self.outfile = None
+            self.process = subprocess.Popen(
+                self._program_args, stderr=self._stderr, stdout=PIPE, **kwargs
+            )  # type: ignore
             self._file: BinaryIO = self.process.stdout  # type: ignore
             self._wait_for_output_or_process_exit()
             self._raise_if_error()
         else:
+            if compresslevel is not None:
+                self._program_args += ["-" + str(compresslevel)]
+            self.outfile = open(path, mode[0] + "b")
+            try:
+                self.process = Popen(
+                    self._program_args,
+                    stderr=self._stderr,
+                    stdin=PIPE,
+                    stdout=self.outfile,
+                    **kwargs,
+                )  # type: ignore
+            except OSError:
+                self.outfile.close()
+                raise
             assert self.process.stdin is not None
             self._file = self.process.stdin  # type: ignore
+
         _set_pipe_size_to_max(self._file.fileno())
 
     def __repr__(self):
@@ -242,35 +263,6 @@ def __repr__(self):
             self._threads,
         )
 
-    def _open_process(
-        self,
-        mode: str,
-        compresslevel: Optional[int],
-        threads: int,
-    ) -> Popen:
-        program_args: List[str] = self._program_args[:]  # prevent list aliasing
-        if threads != 0 and self._threads_flag is not None:
-            program_args += [f"{self._threads_flag}{threads}"]
-
-        if ("w" or "a") in mode and compresslevel is not None:
-            program_args += ["-" + str(compresslevel)]
-
-        if "r" in mode:
-            program_args += ["-c", "-d", self._path]  # type: ignore
-            kwargs = dict(stdout=PIPE)
-        else:
-            kwargs = dict(stdin=PIPE, stdout=self.outfile)  # type: ignore
-
-        # Setting close_fds to True in the Popen arguments is necessary due to
-        # <http://bugs.python.org/issue12786>.
-        # However, close_fds is not supported on Windows. See
-        # <https://github.com/marcelm/cutadapt/issues/315>.
-        if sys.platform != "win32":
-            kwargs["close_fds"] = True
-
-        process = Popen(program_args, stderr=self._stderr, **kwargs)  # type: ignore
-        return process
-
     def write(self, arg: bytes) -> int:
         return self._file.write(arg)