1 files changed, 51 insertions, 11 deletions

diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index be1eac4..2d9e9a8 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -1,12 +1,14 @@
 """Quality control checks for R/qtl2 data bundles."""
-from zipfile import ZipFile
+from pathlib import Path
 from functools import reduce, partial
+from zipfile import ZipFile, is_zipfile
 from typing import Union, Iterator, Optional, Callable
 
-from r_qtl import errors as rqe
 from r_qtl import r_qtl2 as rqtl2
+from r_qtl import exceptions as rqe
 from r_qtl.r_qtl2 import FILE_TYPES
 from r_qtl.fileerrors import MissingFile
+from r_qtl.exceptions import InvalidFormat
 
 from quality_control.errors import InvalidValue
 from quality_control.checks import decimal_points_error
@@ -39,11 +41,10 @@ def bundle_files_list(cdata: dict) -> tuple[tuple[str, str], ...]:
 
     return fileslist
 
-def missing_files(zfile: ZipFile) -> tuple[tuple[str, str], ...]:
-    """
-    Retrieve a list of files listed in the control file that do not exist in the
-    bundle.
-    """
+
+def __missing_from_zipfile__(
+        zfile: ZipFile, cdata: dict) -> tuple[tuple[str, str], ...]:
+    """Check for missing files from a still-compressed zip file."""
     def __missing_p__(filedetails: tuple[str, str]):
         _cfkey, thefile = filedetails
         try:
@@ -52,14 +53,53 @@ def missing_files(zfile: ZipFile) -> tuple[tuple[str, str], ...]:
         except KeyError:
             return True
 
-    return tuple(afile for afile in bundle_files_list(rqtl2.control_data(zfile))
+    return tuple(afile for afile in bundle_files_list(cdata)
                  if __missing_p__(afile))
 
-def validate_bundle(zfile: ZipFile):
+
+def __missing_from_dirpath__(
+        dirpath: Path, cdata: dict) -> tuple[tuple[str, str], ...]:
+    """Check for missing files from an extracted bundle."""
+    allfiles = tuple(_file.name for _file in dirpath.iterdir())
+    return tuple(afile for afile in bundle_files_list(cdata)
+                 if afile[1] not in allfiles)
+
+
+def missing_files(bundlesrc: Union[Path, ZipFile]) -> tuple[tuple[str, str], ...]:
+    """
+    Retrieve a list of files listed in the control file that do not exist in the
+    bundle.
+
+    Parameters
+    ----------
+    bundlesrc: Path object of ZipFile object: This is the bundle under check.
+
+    Returns
+    -------
+    A tuple of names listed in the control file that do not exist in the bundle.
+
+    Raises
+    ------
+    r_qtl.exceptions.InvalidFormat
+    """
+    cdata = rqtl2.control_data(bundlesrc)
+    if isinstance(bundlesrc, ZipFile):
+        return __missing_from_zipfile__(bundlesrc, cdata)
+    if isinstance(bundlesrc, Path):
+        if is_zipfile(bundlesrc):
+            return __missing_from_zipfile__(ZipFile(bundlesrc), cdata)
+        if bundlesrc.is_dir():
+            return __missing_from_dirpath__(bundlesrc, cdata)
+    raise InvalidFormat(
+        "Expects either a zipfile.ZipFile object or a pathlib.Path object "
+        "pointing to a directory containing the R/qtl2 bundle.")
+
+
+def validate_bundle(zfile: Union[Path, ZipFile]):
     """Ensure the R/qtl2 bundle is valid."""
     missing = missing_files(zfile)
     if len(missing) > 0:
-        raise rqe.MissingFileError(
+        raise rqe.MissingFileException(
                         "The following files do not exist in the bundle: " +
                         ", ".join(mfile[1] for mfile in missing))
 
@@ -111,6 +151,6 @@ def retrieve_errors(zfile: ZipFile, filetype: str, checkers: tuple[Callable]) ->
                 if value is not None:
                     for checker in checkers:
                         yield checker(lineno=lineno, field=field, value=value)
-    except rqe.MissingFileError:
+    except rqe.MissingFileException:
         fname = cdata.get(filetype)
         yield MissingFile(filetype, fname, f"Missing '{filetype}' file '{fname}'.")