Merge pull request #10 from bioforensics/checksum

Verify file copies

Author: rnmitchell

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Support for renaming samples while copying (#6)
 - Support for symbolic linking instead of copying (#9)
+- SHA256 checksums to ensure integrity of copied files (#10)
 
 
 ## [0.1.3] 2025-12-03

ezfastq/fastq.py

@@ -8,6 +8,7 @@
 # -------------------------------------------------------------------------------------------------
 
 from dataclasses import dataclass
+from hashlib import sha256
 from pathlib import Path
 from shutil import copy
 from subprocess import run
@@ -42,6 +43,8 @@ def copy(self, destination):
         destination.mkdir(parents=True, exist_ok=True)
         file_copy = destination / self._working_name
         copy(self.source_path, file_copy)
+        if file_sha256(self.source_path) != file_sha256(file_copy):  # pragma: no cover
+            raise CopyError(f"checksum failed for {self.source_path}")
         if self.extension == "fastq":
             run(["gzip", str(file_copy)])
 
@@ -71,5 +74,17 @@ def _working_name(self):
         return f"{self.stem}.{self.extension}"
 
 
+def file_sha256(path, block_size=65536):
+    sha = sha256()
+    with open(path, "rb") as fh:
+        for block in iter(lambda: fh.read(block_size), b""):
+            sha.update(block)
+    return sha.hexdigest()
+
+
+class CopyError(RuntimeError):
+    pass
+
+
 class LinkError(ValueError):
     pass