- added unit test to demonstrate the bug

src/test/data/cml/(1R)-1-aminoethan-1-ol-malformedDictRef.cml

@@ -0,0 +1,30 @@
+<?xml version="1.0" ?>
+<cml>
+    <MDocument>
+        <MChemicalStruct>
+            <!-- A very simple molecule to test bug 1275
+                 - when dictRef is incomplete it should not throw an exception
+            -->
+            <molecule molID="m1">
+                <atomArray>
+                    <atom id="a1" elementType="C"
+                          x2="-1.3200000524520874" y2="-1.815000057220459"/>
+                    <atom id="a2" elementType="N"
+                          x2="0.013679069375948316" y2="-2.585000057220459"/>
+                    <atom id="a3" elementType="C"
+                          x2="-2.6536791742801227" y2="-2.5850000572204594"/>
+                    <atom id="a4" elementType="O"
+                          x2="-1.3200000524520874" y2="-0.27500005722045895"/>
+                </atomArray>
+                <bondArray>
+                    <bond atomRefs2="a1 a2" order="1"/>
+                    <bond atomRefs2="a1 a4" order="1">
+                        <!-- the dictRef is incomplete and should not be used -->
+                        <bondStereo dictRef="cml:">W</bondStereo>
+                    </bond>
+                    <bond atomRefs2="a1 a3" order="1"/>
+                </bondArray>
+            </molecule>
+        </MChemicalStruct>
+    </MDocument>
+</cml>

src/test/org/openscience/cdk/io/CMLReaderTest.java

@@ -188,4 +188,44 @@ public void testBug1274() throws CDKException, IOException {
         }
     }
 
+    /**
+     * Ensures that {@code <bondStereo dictRef="cml:"/>} doesn't cause an exception
+     *
+     * @cdk.bug 1275
+     */
+    @Test
+    public void testBug1275() throws CDKException, IOException {
+
+        InputStream in = getClass().getResourceAsStream("/data/cml/(1R)-1-aminoethan-1-ol-malformedDictRef.cml");
+        CMLReader reader = new CMLReader(in);
+        try {
+            IChemFile cfile = reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IChemFile.class));
+
+
+            Assert.assertNotNull("ChemFile was null", cfile);
+
+            List<IAtomContainer> containers = ChemFileManipulator.getAllAtomContainers(cfile);
+
+            Assert.assertEquals("expected a single atom container", 1, containers.size());
+
+            IAtomContainer container = containers.get(0);
+
+            Assert.assertNotNull("null atom container read", container);
+
+            // we check here that the malformed dictRef doesn't throw an exception
+            Assert.assertEquals("expected non-stereo bond",
+                                IBond.Stereo.NONE, container.getBond(0).getStereo());
+            Assert.assertEquals("expected Wedge (Up) Bond",
+                                IBond.Stereo.UP, container.getBond(1).getStereo());
+            Assert.assertEquals("expected non-stereo bond",
+                                IBond.Stereo.NONE, container.getBond(2).getStereo());
+
+        } finally {
+            reader.close();
+        }
+
+    }
+
+
+
 }