Merge pull request #223 from cadenmyers13/check-saved-files

feat: Check if saved files exists and raise an early error if they do

Author: sbillinge

docs/source/examples/labpdfprocapp-example.rst

@@ -77,15 +77,15 @@ For example,
     labpdfproc mud zro2_mo.xy 2.5 -w 0.71303
     labpdfproc mud zro2_mo.xy 2.5 -w Mo
 
-This will then save the corrected file in the same directory as the input file with the name ``zro2_mo_corrected.chi``.
+This will then save the corrected file in the same directory as the input file with the name ``zro2_mo-mud-corrected.chi``.
 
 To save the correction file, specify the ``-c`` or ``--output-correction`` flag,
 
 .. code-block:: bash
 
     labpdfproc mud zro2_mo.xy 2.5 -w 0.71303 -c
 
-This will then save the correction file in the same directory as the input file with the name ``zro2_mo_cve.chi``.
+This will then save the correction file in the same directory as the input file with the name ``zro2_mo-cve.chi``.
 
 ``labpdfproc zscan`` Command
 ----------------------------
@@ -123,7 +123,7 @@ To save the correction file, specify the ``-c`` or ``--output-correction`` flag,
 
     labpdfproc zscan CeO2_635um_accum_0.xy CeO2_635um_zscan.xy -w 0.71303 -c
 
-This will then save the correction file in the same directory as the input file with the name ``CeO2_635um_accum_0_cve.chi``.
+This will then save the correction file in the same directory as the input file with the name ``CeO2_635um_accum_0-cve.chi``.
 
 ``labpdfproc sample`` Command
 -----------------------------
@@ -163,7 +163,7 @@ To save the correction file, specify the ``-c`` or ``--output-correction`` flag,
 
     labpdfproc sample zro2_mo.xy ZrO2 17.45 1.2 -w 0.71303 -c
 
-This will then save the correction file in the same directory as the input file with the name ``zro2_mo_cve.chi``.
+This will then save the correction file in the same directory as the input file with the name ``zro2_mo-cve.chi``.
 
 Additional CLI options
 ----------------------

news/check-saved-files.rst

@@ -0,0 +1,25 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Changed output file behavior to raise an error early if the saved file exists.
+* Changed saved file name from ``_corrected.chi`` to ``-mud-corrected.chi``.
+* Changed saved file name from ``_cve.chi`` to ``-cve.chi``.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -131,20 +131,14 @@ def _add_credit_args(parser, use_gui=False):
 
 
 def _save_corrected(corrected, input_path, args):
-    outfile = args.output_directory / (input_path.stem + "_corrected.chi")
-    if outfile.exists() and not args.force:
-        print(f"WARNING: {outfile} exists. Use --force to overwrite.")
-        return
+    outfile = args.output_directory / (f"{input_path.stem}-mud-corrected.chi")
     corrected.metadata = corrected.metadata or {}
     corrected.dump(str(outfile), xtype=args.xtype)
     print(f"Saved corrected data to {outfile}")
 
 
 def _save_correction(correction, input_path, args):
-    corrfile = args.output_directory / (input_path.stem + "_cve.chi")
-    if corrfile.exists() and not args.force:
-        print(f"WARNING: {corrfile} exists. Use --force to overwrite.")
-        return
+    corrfile = args.output_directory / (f"{input_path.stem}-cve.chi")
     correction.metadata = correction.metadata or {}
     correction.dump(str(corrfile), xtype=args.xtype)
     print(f"Saved correction data to {corrfile}")
@@ -312,7 +306,9 @@ def get_args_gui():
 
 def get_args_cli(override=None):
     parser = create_parser(use_gui=False)
-    return parser.parse_args(override)
+    argv = override if override is not None else sys.argv[1:]
+    argv = [arg for arg in argv if arg != "--ignore-gooey"]
+    return parser.parse_args(argv)
 
 
 def main():

src/diffpy/labpdfproc/tools.py

@@ -528,6 +528,27 @@ def load_package_info(args):
     return args
 
 
+def _check_saved_file_exists(args):
+    """Check if the output files already exist based on the input paths
+    and output directory."""
+    existing_files = []
+    for path in args.input_paths:
+        outfile = args.output_directory / (f"{path.stem}-mud-corrected.chi")
+        if outfile.exists() and not args.force:
+            existing_files.append(outfile)
+        if args.output_correction:
+            corrfile = args.output_directory / (f"{path.stem}-cve.chi")
+            if corrfile.exists() and not args.force:
+                existing_files.append(corrfile)
+    if existing_files:
+        existing_files_str = "\n".join(str(f) for f in existing_files)
+        raise FileExistsError(
+            "The following output files already exist:"
+            f"\n{existing_files_str}\n"
+            "Use --force to overwrite them."
+        )
+
+
 def preprocessing_args(args):
     """Perform preprocessing on the provided args. The process includes
     loading package and user information, setting input, output,
@@ -542,6 +563,11 @@ def preprocessing_args(args):
     -------
     args : argparse.Namespace
         The updated argparse Namespace with arguments preprocessed.
+
+    Raises
+    ------
+    FileExistsError
+        If the output files already exist and --force is not used.
     """
     args = load_wavelength_from_config_file(args)
     args = set_mud(args)
@@ -552,6 +578,7 @@ def preprocessing_args(args):
     args = load_user_metadata(args)
     args = load_user_info(args)
     args = load_package_info(args)
+    _check_saved_file_exists(args)
     return args
 
 

tests/conftest.py

@@ -13,7 +13,8 @@ def user_filesystem(tmp_path):
     home_dir.mkdir(parents=True, exist_ok=True)
     test_dir = base_dir / "test_dir"
     test_dir.mkdir(parents=True, exist_ok=True)
-
+    output_dir = base_dir / "output_dir"
+    output_dir.mkdir(parents=True, exist_ok=True)
     chi_data = (
         "dataformat = twotheta\n mode = "
         "xray\n # chi_Q chi_I\n 1 2\n 3 4\n 5 6\n 7 8\n"
@@ -59,6 +60,10 @@ def user_filesystem(tmp_path):
         f.write("good_data.xy \n")
         f.write(f"{str(input_dir.resolve() / 'good_data.txt')}\n")
 
+    with open(output_dir / "good_data-mud-corrected.chi", "w") as f:
+        f.write(chi_data)
+    with open(output_dir / "good_data-cve.chi", "w") as f:
+        f.write(chi_data)
     home_config_data = {
         "wavelength": 0.3,
         "owner_name": "home_username",

tests/test_tools.py

@@ -847,3 +847,38 @@ def test_load_metadata(mocker, user_filesystem, inputs, expected):
             **expected,
         }
         assert actual_metadata == expected_metadata
+
+
+def test_preprocess_args_bad(user_filesystem, monkeypatch):
+    # Case: user tries to run absorption correction, but the output
+    # filenames already for *-mud-corrected.chi and *-cve.chi exists.
+    # expected: preprocess_args catches this early and raises an Error
+    cwd = Path(user_filesystem)
+    home_dir = cwd / "home_dir"
+    # set cwd so program can find diffpyconfig.json
+    monkeypatch.setattr("pathlib.Path.home", lambda _: home_dir)
+    input_data_file = str(user_filesystem / "good_data.chi")
+    existing_corrected_file = str(
+        user_filesystem / "output_dir" / "good_data-mud-corrected.chi"
+    )
+    existing_corrected_cve_file = str(
+        user_filesystem / "output_dir" / "good_data-cve.chi"
+    )
+    cli_inputs = [
+        "mud",
+        input_data_file,
+        "2.5",
+        "-o",
+        str(user_filesystem / "output_dir"),
+        "-c",  # -c flag saves the cve file
+    ]
+    args = get_args_cli(cli_inputs)
+    args = set_input_lists(args)
+    msg = (
+        "The following output files already exist:"
+        f"\n{existing_corrected_file}\n"
+        f"{existing_corrected_cve_file}\n"
+        "Use --force to overwrite them."
+    )
+    with pytest.raises(FileExistsError, match=re.escape(msg)):
+        preprocessing_args(args)