reading mmJSON: don't crash on empty array (#336)

project-gemmi · Sep 19, 2024 · 2963d1f · 2963d1f
1 parent 2fa3b93
commit 2963d1f
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Showing 2 changed files with 10 additions and 3 deletions.
diff --git a/src/json.cpp b/src/json.cpp
@@ -98,7 +98,7 @@ static void fill_document_from_sajson(Document& d, const sajson::document& s) {
              std::to_string(arr.get_length()));
       if (cif_rows == 1) {
         items.emplace_back(tag, as_cif_value(arr.get_array_element(0)));
-      } else {
+      } else if (cif_rows != 0) {
         Loop& loop = items.back().loop;
         loop.tags.emplace_back(std::move(tag));
         for (size_t k = 0; k != cif_rows; ++k)

diff --git a/tests/test_mol.py b/tests/test_mol.py
@@ -427,14 +427,21 @@ def test_previous_next_residue(self):
     def test_read_1pfe_cif(self):
         st = gemmi.read_structure(full_path('1pfe.cif.gz'))
         self.check_1pfe(st)
+        mmcif_doc = st.make_mmcif_document()
 
-        # write structure to cif and read it back
+        # write structure to cif file and read it back
         out_name = get_path_for_tempfile(suffix='.cif')
-        st.make_mmcif_document().write_file(out_name)
+        mmcif_doc.write_file(out_name)
         st2 = gemmi.read_structure(out_name)
         os.remove(out_name)
         self.check_1pfe(st2)
 
+        # write structure to mmJSON string and read it back
+        json_str = mmcif_doc.as_json(mmjson=True)
+        doc = gemmi.cif.read_mmjson_string(json_str)
+        st3 = gemmi.make_structure_from_block(doc[0])
+        self.check_1pfe(st3)
+
     def test_read_1pfe_json(self):
         st = gemmi.read_structure(full_path('1pfe.json'))
         self.check_1pfe(st)