From ab71b34b97f3f1eee52b5688f41644541535f281 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 5 Feb 2024 07:00:01 +0300
Subject: Do general bundle validation and show errors

* Display any and all errors on the UI
* Move `validate_bundle` to QC module and refactor to use
  `missing_files`
---
 r_qtl/r_qtl2.py | 22 ----------------------
 1 file changed, 22 deletions(-)

(limited to 'r_qtl/r_qtl2.py')

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index c2828d2..f8c08d9 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -288,28 +288,6 @@ def sex_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
             key: chain(value, partial(replace_sex_info, cdata=cdata))
             for key, value in row.items() if key not in ci_fields}
 
-def validate_bundle(zfile: ZipFile):
-    """Ensure the R/qtl2 bundle is valid."""
-    cdata = control_data(zfile)
-    def __member_exists_p__(zfile, member):
-        if isinstance(member, str):
-            zfile.getinfo(member)
-        else:
-            for inner in member:
-                zfile.getinfo(inner)
-
-    try:
-        for member in (key for key in cdata.keys() if key in __FILE_TYPES__):
-            __member_exists_p__(zfile, cdata[member])
-
-        if "file" in cdata.get("sex", {}):
-            __member_exists_p__(zfile, cdata["sex"]["file"])
-
-        if "file" in cdata.get("cross_info", {}):
-            __member_exists_p__(zfile, cdata["cross_info"]["file"])
-    except KeyError as kerr:
-        raise InvalidFormat(*kerr.args) from kerr
-
 def genotype_data(zfile: ZipFile):
     """Convenience function to genotype data from R/qtl2 bundle."""
     cdata = control_data(zfile)
-- 
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