Add a hidden argument to retain the tempdir

Add spaces around input files in commands. Fixes shell parsing for input files with spaces
Sentieon · Jan 5, 2024 · 0a79561 · 0a79561
1 parent d12f377
commit 0a79561
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Showing 3 changed files with 17 additions and 11 deletions.
diff --git a/sentieon_cli/__init__.py b/sentieon_cli/__init__.py
@@ -30,7 +30,7 @@
 def tmp():
     """Create a temporary directory for the current process."""
     tmp_base = os.getenv("SENTIEON_TMPDIR")
-    tmp_dir = tempfile.TemporaryDirectory(dir=tmp_base)
+    tmp_dir = tempfile.mkdtemp(dir=tmp_base)
     return tmp_dir
 
 
@@ -165,6 +165,10 @@ def _path_arg(arg: str) -> pathlib.Path:
     "--skip-version-check",
     help=argparse.SUPPRESS,
 )
+@arg(
+    "--retain-tmpdir",
+    help=argparse.SUPPRESS,
+)
 def dnascope_longread(
     output_vcf: pathlib.Path,
     reference: Optional[pathlib.Path] = None,
@@ -178,6 +182,7 @@ def dnascope_longread(
     dry_run: bool = False,
     repeat_model: Optional[pathlib.Path] = None,
     skip_version_check: bool = False,
+    retain_tmpdir: bool = False,
     **kwargs: str,
 ):
     """
@@ -194,8 +199,8 @@ def dnascope_longread(
         for cmd, min_version in TOOL_MIN_VERSIONS.items():
             check_version(cmd, min_version)
 
-    tmp_dir_obj = tmp()
-    tmp_dir = pathlib.Path(tmp_dir_obj.name)
+    tmp_dir_str = tmp()
+    tmp_dir = pathlib.Path(tmp_dir_str)
 
     if dry_run:
         run = print
@@ -440,7 +445,8 @@ def dnascope_longread(
             )
         )
 
-    shutil.rmtree(tmp_dir)
+    if not retain_tmpdir:
+        shutil.rmtree(tmp_dir_str)
     return
 
 

diff --git a/sentieon_cli/command_strings.py b/sentieon_cli/command_strings.py
@@ -36,13 +36,13 @@ def build_cmd(self) -> List[str]:
             elif isinstance(v, list):
                 for i in v:
                     cmd.append(f"--{k}")
-                    cmd.append(str(i))
+                    cmd.append(f"'{i}'")
             elif isinstance(v, bool):
                 if v:
                     cmd.append(f"--{k}")
             else:
                 cmd.append(f"--{k}")
-                cmd.append(str(v))
+                cmd.append(f"'{v}'")
 
         if "output" in self.__dict__:
             cmd.append(str(self.__dict__["output"]))
@@ -183,13 +183,13 @@ def build_cmd(self) -> List[str]:
             elif isinstance(v, list):
                 for i in v:
                     cmd.append(f"--{k}")
-                    cmd.append(str(i))
+                    cmd.append(f"'{i}'")
             elif isinstance(v, bool):
                 if v:
                     cmd.append(f"--{k}")
             else:
                 cmd.append(f"--{k}")
-                cmd.append(str(v))
+                cmd.append(f"'{v}'")
 
         for algo in self.algo:
             cmd.extend(algo.build_cmd())

diff --git a/tests/test_all.py b/tests/test_all.py
@@ -18,9 +18,9 @@ def test_one():
 def test_tmp():
     """basic test for tmp()"""
     tmp_dir = sentieon_cli.tmp()
-    assert os.path.exists(tmp_dir.name)
-    assert os.path.isdir(tmp_dir.name)
-    shutil.rmtree(tmp_dir.name)
+    assert os.path.exists(tmp_dir)
+    assert os.path.isdir(tmp_dir)
+    shutil.rmtree(tmp_dir)
 
 
 def test_find_script():