Add flag to skip renaming files

imagedephi/gui.py

@@ -63,7 +63,7 @@ async def lifespan(app: FastAPI) -> AsyncGenerator[None, None]:
 templates = Jinja2Templates(
     # Jinja2Templates requires a "directory" argument, but it is effectively unused
     # if a custom loader is passed
-    directory="",
+    directory=".",
     loader=FunctionLoader(_load_template),
 )
 

imagedephi/main.py

@@ -111,12 +111,21 @@ def imagedephi(
     help="Path where output directory will be created.",
     type=click.Path(exists=True, file_okay=False, readable=True, writable=True, path_type=Path),
 )
+@click.option("--rename/--skip-rename", default=True)
 @click.pass_obj
-def run(obj: ImagedephiContext, input_path: Path, output_dir: Path, verbose, quiet, log_file):
+def run(
+    obj: ImagedephiContext,
+    input_path: Path,
+    output_dir: Path,
+    rename: bool,
+    verbose,
+    quiet,
+    log_file,
+):
     """Perform the redaction of images."""
     if verbose or quiet or log_file:
         set_logging_config(verbose, quiet, log_file)
-    redact_images(input_path, output_dir, obj.override_rule_set)
+    redact_images(input_path, output_dir, obj.override_rule_set, rename)
 
 
 @imagedephi.command

imagedephi/redact/redact.py

@@ -69,6 +69,7 @@ def redact_images(
     input_path: Path,
     output_dir: Path,
     override_rules: Ruleset | None = None,
+    rename: bool = True,
     overwrite: bool = False,
 ) -> None:
     base_rules = get_base_rules()
@@ -96,12 +97,16 @@ def redact_images(
                     redaction_plan.report_missing_rules()
                 else:
                     redaction_plan.execute_plan()
-                    output_path = _get_output_path(
-                        image_file,
-                        redact_dir,
-                        output_file_name_base,
-                        output_file_counter,
-                        output_file_max,
+                    output_path = (
+                        _get_output_path(
+                            image_file,
+                            redact_dir,
+                            output_file_name_base,
+                            output_file_counter,
+                            output_file_max,
+                        )
+                        if rename
+                        else redact_dir / image_file.name
                     )
                     redaction_plan.save(output_path, overwrite)
                     if output_file_counter == output_file_max:

imagedephi/utils/logger.py

@@ -9,7 +9,7 @@
         if os.path.exists("logging.conf")
         else str(importlib.resources.files("imagedephi") / "logging.conf")
     )
-except KeyError:
+except (FileNotFoundError, KeyError):
     pass
 
 logger = logging.getLogger("root")

tests/test_e2e.py

@@ -131,3 +131,23 @@ def test_e2e_help(cli_runner: CliRunner, help_flag: str) -> None:
 
     assert result.exit_code == 0
     assert "Usage: imagedephi" in result.output
+
+
+@freeze_time("2023-05-12 12:12:53")
+@pytest.mark.timeout(5)
+@pytest.mark.parametrize("rename", [True, False])
+def test_e2e_rename_flag(cli_runner, data_dir: Path, tmp_path: Path, rename: bool):
+    rename_flag = "--rename" if rename else "--skip-rename"
+    result = cli_runner.invoke(
+        main.imagedephi,
+        ["run", str(data_dir / "input" / "tiff"), "--output-dir", str(tmp_path), rename_flag],
+    )
+
+    assert result.exit_code == 0
+
+    output_file_name = (
+        tmp_path / "Redacted_2023-05-12_12-12-53" / "study_slide_1.tif"
+        if rename
+        else tmp_path / "Redacted_2023-05-12_12-12-53" / "test_image.tif"
+    )
+    assert output_file_name.exists()