From dd369b846524fed0c08d1b7318fd73478506c3ee Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 9 Feb 2024 03:10:06 +0300
Subject: Provide the key for each file listed in the control file.

---
 r_qtl/r_qtl2_qc.py | 32 ++++++++++++++++++--------------
 1 file changed, 18 insertions(+), 14 deletions(-)

(limited to 'r_qtl')

diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index 4b3e184..a41c442 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -2,7 +2,7 @@
 import re
 from zipfile import ZipFile
 from functools import reduce
-from typing import Union, Sequence, Iterator, Optional, Callable
+from typing import Union, Iterator, Optional, Callable
 
 from r_qtl import errors as rqe
 from r_qtl import r_qtl2 as rqtl2
@@ -11,14 +11,15 @@ from r_qtl.fileerrors import MissingFile
 
 from quality_control.errors import InvalidValue
 
-def bundle_files_list(cdata: dict) -> tuple[str, ...]:
+def bundle_files_list(cdata: dict) -> tuple[tuple[str, str], ...]:
     """Retrieve files listed in control file."""
-    def __merge__(alist: tuple[str, ...], member: Union[str, Sequence[str]]) -> tuple[str, ...]:
+    def __merge__(alist: tuple[tuple[str, str], ...], member: str) -> tuple[
+            tuple[str, str], ...]:
         if isinstance(cdata[member], str):
-            return alist + (cdata[member],)
-        return alist + tuple(cdata[member])
+            return alist + ((member, str(cdata[member])),)
+        return alist + tuple((member, str(afile)) for afile in cdata[member])
 
-    fileslist: tuple[str, ...] = reduce(
+    fileslist: tuple[tuple[str, str], ...] = reduce(
         __merge__,
         (key for key in cdata.keys() if key in __FILE_TYPES__),
         tuple())
@@ -26,30 +27,33 @@ def bundle_files_list(cdata: dict) -> tuple[str, ...]:
     if "file" in cdata.get("sex", {}):
         sexfile = cdata["sex"]["file"]
         fileslist = fileslist + (
-            (sexfile,) if isinstance(sexfile, str) else tuple(sexfile))
+            (("sex.file", sexfile),) if isinstance(sexfile, str)
+            else tuple(("sex.file", afile) for afile in sexfile))
 
     if "file" in cdata.get("cross_info", {}):
         crossinfofile = cdata["cross_info"]["file"]
         fileslist = fileslist + (
-            (crossinfofile,) if isinstance(crossinfofile, str)
-            else tuple(crossinfofile))
+            (("cross_info.file", crossinfofile),)
+            if isinstance(crossinfofile, str)
+            else tuple(("cross_info.file", afile) for afile in crossinfofile))
 
     return fileslist
 
-def missing_files(zfile: ZipFile) -> tuple[str, ...]:
+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_p__(thefile):
+    def __missing_p__(filedetails: tuple[str, str]):
+        _cfkey, thefile = filedetails
         try:
             zfile.getinfo(thefile)
             return False
         except KeyError:
             return True
 
-    return tuple(filter(__missing_p__,
-                        bundle_files_list(rqtl2.control_data(zfile))))
+    return tuple(afile for afile in bundle_files_list(rqtl2.control_data(zfile))
+                 if __missing_p__(afile))
 
 def validate_bundle(zfile: ZipFile):
     """Ensure the R/qtl2 bundle is valid."""
@@ -57,7 +61,7 @@ def validate_bundle(zfile: ZipFile):
     if len(missing) > 0:
         raise rqe.MissingFileError(
                         "The following files do not exist in the bundle: " +
-                        ", ".join(missing))
+                        ", ".join(mfile[1] for mfile in missing))
 
 def make_genocode_checker(genocode: dict) -> Callable[[int, str, str], Optional[InvalidValue]]:
     """Make a checker from the genotypes in the control data"""
-- 
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