perform checksum check as part of the app fixes #3

src/depiction/persistence/imzml_read_file.py

@@ -164,8 +164,8 @@ def summary(self, checksums: bool = True) -> str:
             f"{mz_range_line}"
         )
 
-    def print_summary(self, checksums: bool = True) -> None:
-        print(self.summary(checksums=checksums))
+    def print_summary(self, checksums: bool = True, file=None) -> None:
+        print(self.summary(checksums=checksums), file=file)
 
     @cached_property
     def pixel_size(self) -> PixelSize | None:

src/depiction_targeted_preproc/app/entrypoint.py

@@ -11,6 +11,7 @@
 from loguru import logger
 
 from depiction.misc.find_file_util import find_one_by_extension
+from depiction.persistence import ImzmlReadFile
 from depiction_targeted_preproc.pipeline.setup import setup_workdir
 from depiction_targeted_preproc.pipeline_config.artifacts_mapping import ARTIFACT_FILES_MAPPING, get_result_files
 from depiction_targeted_preproc.pipeline_config.model import (
@@ -42,6 +43,9 @@ def entrypoint(
     if not workunit_yaml_file.exists():
         raise RuntimeError(f"Workunit yaml file not found: {workunit_yaml_file}")
 
+    # Ensure the input file's checksum passes
+    check_imzml_file(ImzmlReadFile(input_imzml_file))
+
     # Parse the params
     params = parse_parameters(workunit_yaml_file)
 
@@ -77,6 +81,14 @@ def export_pipeline_params(work_dir: Path, output_dir: Path, sample_name: str) -
     shutil.copy(work_dir / sample_name / "pipeline_params.yml", output_dir / sample_name / "pipeline_params.yml")
 
 
+def check_imzml_file(imzml_file: ImzmlReadFile) -> None:
+    # TODO this is not very efficient, but is better than not checking the file at all
+    logger.info(f"Checking the integrity of the input file: {imzml_file.imzml_file}")
+    logger.info(imzml_file.summary())
+    if not imzml_file.is_checksum_valid:
+        raise RuntimeError(f"Checksum validation failed for the input file: {imzml_file.imzml_file}")
+
+
 def zip_results(output_dir: Path, sample_name: str) -> None:
     with ZipFile(output_dir / f"{sample_name}.zip", "w") as zipf:
         for file in (output_dir / sample_name).rglob("*"):

tests/unit/persistence/test_imzml_read_file.py

@@ -228,7 +228,7 @@ def test_summary_when_continuous(self, method_reader) -> None:
     def test_print_summary(self, mock_summary, mock_print) -> None:
         self.mock_read_file.print_summary()
         mock_summary.assert_called_once_with(checksums=True)
-        mock_print.assert_called_once_with(mock_summary.return_value)
+        mock_print.assert_called_once_with(mock_summary.return_value, file=None)
 
     @patch.object(ImzmlReadFile, "reader")
     def test_cached_properties(self, method_reader) -> None: