added unit test to demonstrate bug and correct bug id's for two recen…

…ts tests

Change-Id: If2c12c6dfaad4c7664b5ec6d439f8ddbec9f2ae9
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

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

@@ -0,0 +1,33 @@
+<?xml version="1.0" ?>
+<cml>
+    <MDocument>
+        <MChemicalStruct>
+            <!-- A very simple molecule to test bug 1274
+                - The bondStereo should use the dictRef attribute when both dictRef and
+                  charContent is available.
+                - The bond stereo should only be set for this single bond
+            -->
+            <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">
+                        <!-- this is bad formatting - but we should favour the dictRef
+                             a logging error should shown for this case -->
+                        <bondStereo dictRef="cml:H">W</bondStereo>
+                    </bond>
+                    <bond atomRefs2="a1 a3" order="1"/>
+                </bondArray>
+            </molecule>
+        </MChemicalStruct>
+    </MDocument>
+</cml>

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

@@ -2,9 +2,9 @@
 <cml>
     <MDocument>
         <MChemicalStruct>
-            <!-- A very molecule to test bug 3553328 and 3557907
-                 - 3553328: Atoms missing explicit atomic number default to 1.
-                 - 3557907: Only support for bond stereo with attribute dictRef
+            <!-- A very simple molecule to test bug 1245 and 1248
+                 - 1245: Atoms missing explicit atomic number default to 1.
+                 - 1248: Only support for bond stereo with attribute dictRef
             -->
             <molecule molID="m1">
                 <atomArray>

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

@@ -36,6 +36,7 @@
 import org.openscience.cdk.tools.periodictable.PeriodicTable;
 
 import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.util.List;
@@ -70,7 +71,7 @@ public void testSetReader_Reader() throws Exception {
      * Ensure stereoBond content is read if the usual "dictRef" attribute is not
      * supplied
      *
-     * @cdk.bug 3557907
+     * @cdk.bug 1248
      */
     @Test
     public void testBug3557907() throws FileNotFoundException, CDKException {
@@ -102,7 +103,7 @@ public void testBug3557907() throws FileNotFoundException, CDKException {
     /**
      * Ensure correct atomic numbers are read and does not default to 1
      *
-     * @cdk.bug 3553328
+     * @cdk.bug 1245
      */
     @Test
     public void testBug3553328() throws FileNotFoundException, CDKException {
@@ -126,6 +127,65 @@ public void testBug3553328() throws FileNotFoundException, CDKException {
                                 PeriodicTable.getAtomicNumber(atom.getSymbol()),
                                 atom.getAtomicNumber());
         }
+    }
 
+    /**
+     * Ensures that when multiple stereo is set the dictRef is favoured
+     * and the charContent is not used. Here is an example of what we expect
+     * to read.
+     *
+     * <pre>{@code
+     * <bond atomRefs2="a1 a4" order="1">
+     *     <bondStereo dictRef="cml:W"/> <!-- should be W -->
+     * </bond>
+     *
+     * <bond atomRefs2="a1 a4" order="1">
+     *     <bondStereo>W</bondStereo> <!-- should be W -->
+     * </bond>
+     *
+     * <bond atomRefs2="a1 a4" order="1">
+     *    <bondStereo dictRef="cml:W">W</bondStereo> <!-- should be W -->
+     * </bond>
+     *
+     * <bond atomRefs2="a1 a4" order="1">
+     *    <bondStereo dictRef="cml:W">H</bondStereo> <!-- should be W -->
+     * </bond>
+     * }</pre>
+     *
+     * @cdk.bug 1274
+     * @see #testBug1248()
+     */
+    @Test
+    public void testBug1274() throws CDKException, IOException {
+
+        InputStream in = getClass().getResourceAsStream("/data/cml/(1R)-1-aminoethan-1-ol-multipleBondStereo.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 charContent is not used and also that more then
+            // one stereo isn't set
+            Assert.assertEquals("expected non-stereo bond",
+                                IBond.Stereo.NONE, container.getBond(0).getStereo());
+            Assert.assertEquals("expected Hatch (Down) Bond",
+                                IBond.Stereo.DOWN, container.getBond(1).getStereo());
+            Assert.assertEquals("expected non-stereo bond",
+                                IBond.Stereo.NONE, container.getBond(2).getStereo());
+
+        } finally {
+            reader.close();
+        }
     }
+
 }