From 2e6953fd06cfe9d8befbab54368b48849079f780 Mon Sep 17 00:00:00 2001
From: seth <getchoo@tuta.io>
Date: Thu, 9 May 2024 15:12:34 -0400
Subject: [PATCH] python311Packages.biopython: patch SeqXMLIO parser

---
 .../biopython/close_parser_on_time.patch       | 18 ++++++++++++++++++
 .../python-modules/biopython/default.nix       |  7 +++++++
 2 files changed, 25 insertions(+)
 create mode 100644 pkgs/development/python-modules/biopython/close_parser_on_time.patch

diff --git a/pkgs/development/python-modules/biopython/close_parser_on_time.patch b/pkgs/development/python-modules/biopython/close_parser_on_time.patch
new file mode 100644
index 000000000000..05d22e22ed9e
--- /dev/null
+++ b/pkgs/development/python-modules/biopython/close_parser_on_time.patch
@@ -0,0 +1,18 @@
+diff --git a/Bio/SeqIO/SeqXmlIO.py b/Bio/SeqIO/SeqXmlIO.py
+index 8fe75ebb728..6758317d05f 100644
+--- a/Bio/SeqIO/SeqXmlIO.py
++++ b/Bio/SeqIO/SeqXmlIO.py
+@@ -498,11 +498,12 @@ def iterate(self, handle):
+             if not text:
+                 break
+             parser.feed(text)
++        # Closing the parser ensures that all XML data fed into it are processed
++        parser.close()
+         # We have reached the end of the XML file;
+         # send out the remaining records
+         yield from records
+         records.clear()
+-        parser.close()
+ 
+ 
+ class SeqXmlWriter(SequenceWriter):
diff --git a/pkgs/development/python-modules/biopython/default.nix b/pkgs/development/python-modules/biopython/default.nix
index 2ec814f56aef..2baa052011d5 100644
--- a/pkgs/development/python-modules/biopython/default.nix
+++ b/pkgs/development/python-modules/biopython/default.nix
@@ -18,6 +18,13 @@ buildPythonPackage rec {
     hash = "sha256-eOa/t43mMDQDev01/nfLbgqeW2Jwa+z3in2SKxbtg/c=";
   };
 
+  patches = [
+    # cherry-picked from https://github.com/biopython/biopython/commit/3f9bda7ef44f533dadbaa0de29ac21929bc0b2f1
+    # fixes SeqXMLIO parser to process all data. remove on next update
+    ./close_parser_on_time.patch
+  ];
+
+
   nativeBuildInputs = [
     setuptools
   ];