From c11caffbd765d798e383fe558675771a2e2edc0d Mon Sep 17 00:00:00 2001
From: James Thompson <thompj@google.com>
Date: Tue, 17 Dec 2024 15:26:41 +0000
Subject: [PATCH] Vulnerability fixes

---
 Code/GraphMol/FileParsers/MolSGroupParsing.cpp | 10 ++++++++++
 Code/GraphMol/SmilesParse/CXSmilesOps.cpp      |  3 ++-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/Code/GraphMol/FileParsers/MolSGroupParsing.cpp b/Code/GraphMol/FileParsers/MolSGroupParsing.cpp
index f02366f22..330387b45 100644
--- a/Code/GraphMol/FileParsers/MolSGroupParsing.cpp
+++ b/Code/GraphMol/FileParsers/MolSGroupParsing.cpp
@@ -1132,7 +1132,17 @@ void ParseV3000ParseLabel(const std::string &label,
     } else if (label == "PARENT") {
       // Store relationship until all SGroups have been read
       unsigned int parentIdx;
+      if (lineStream.eof()) {
+        std::ostringstream errout;
+        errout << "PARENT label not found on line " << line;
+        throw FileParseException(errout.str());
+      }
       lineStream >> parentIdx;
+      if (lineStream.fail()) {
+        std::ostringstream errout;
+        errout << "Invalid PARENT label found on line " << line;
+        throw FileParseException(errout.str());
+      }
       sgroup.setProp<unsigned int>("PARENT", parentIdx);
     } else if (label == "COMPNO") {
       unsigned int compno;
diff --git a/Code/GraphMol/SmilesParse/CXSmilesOps.cpp b/Code/GraphMol/SmilesParse/CXSmilesOps.cpp
index ee58181a9..4525f67f0 100644
--- a/Code/GraphMol/SmilesParse/CXSmilesOps.cpp
+++ b/Code/GraphMol/SmilesParse/CXSmilesOps.cpp
@@ -692,6 +692,7 @@ template <typename Iterator>
 void parse_data_sgroup_attr(Iterator &first, Iterator last,
                             SubstanceGroup &sgroup, bool keepSGroup,
                             std::string fieldName, bool fieldIsArray = false) {
+  PRECONDITION(first < last);
   if (first != last && *first != '|') {
     std::string data = read_text_to(first, last, ":");
     ++first;
@@ -744,7 +745,7 @@ bool parse_data_sgroup(Iterator &first, Iterator last, RDKit::RWMol &mol,
   }
 
   parse_data_sgroup_attr(first, last, sgroup, keepSGroup, "DATAFIELDS", true);
-
+  
   parse_data_sgroup_attr(first, last, sgroup, keepSGroup, "QUERYOP");
 
   parse_data_sgroup_attr(first, last, sgroup, keepSGroup, "FIELDINFO");