From 8595c75345fb5849a4d8894f3ee7a926dd8cdf8f Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 8 Jan 2024 07:25:35 +0300
Subject: Upload R/qtl2 zip bundle and check for errors.

---
 r_qtl/r_qtl2.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'r_qtl')

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 2c1e162..a8958a0 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -242,3 +242,27 @@ def sex_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
         yield {
             key: thread_op(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 (
+                "geno", "founder_geno", "pheno", "covar", "phenocovar", "gmap",
+                "pmap")):
+            __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
-- 
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