Fix crash when reading cjson with invalid layer data (#1636)

* Fix crash when reading cjson with invalid layer data If a script adds atoms or bonds, but not layers, it's skipped Signed-off-by: Geoff Hutchison <[email protected]>
OpenChemistry · Mar 2, 2024 · 7061aac · 7061aac
1 parent 12e5606
commit 7061aac
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diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -8,7 +8,7 @@ concurrency:
 
 env:
   # Don't build python 2.7, pypy, or 32-bit wheels or Mac arm64 on Py3.8
-  CIBW_SKIP: "cp36-* cp37-* cp311-* cp38-macosx_arm64 pp* *-musllinux_* *-manylinux_i686 *-win32"
+  CIBW_SKIP: "cp36-* cp37-* cp311-manylinux* cp312-manylinux* cp38-macosx_arm64 pp* *-musllinux_* *-manylinux_i686 *-win32"
 
   # Need to do some setup before repairing the wheel on linux...
   CIBW_REPAIR_WHEEL_COMMAND_LINUX: bash scripts/github-actions/repair_command_linux.sh

diff --git a/avogadro/io/cjsonformat.cpp b/avogadro/io/cjsonformat.cpp
@@ -215,7 +215,7 @@ bool CjsonFormat::deserialize(std::istream& file, Molecule& molecule,
     json layerJson = atoms["layer"];
     if (isNumericArray(layerJson)) {
       auto& layer = LayerManager::getMoleculeInfo(&molecule)->layer;
-      for (Index i = 0; i < atomCount; ++i) {
+      for (Index i = 0; i < atomCount && i < layerJson.size(); ++i) {
         while (layerJson[i] > layer.maxLayer()) {
           layer.addLayer();
         }
@@ -242,8 +242,9 @@ bool CjsonFormat::deserialize(std::istream& file, Molecule& molecule,
 
     // are there bond labels?
     json bondLabels = bonds["labels"];
-    if (bondLabels.is_array() && bondLabels.size() == molecule.bondCount()) {
-      for (unsigned int i = 0; i < molecule.bondCount(); ++i) {
+    if (bondLabels.is_array()) {
+      for (unsigned int i = 0;
+           i < molecule.bondCount() && i < bondLabels.size(); ++i) {
         molecule.setBondLabel(i, bondLabels[i]);
       }
     }