Test SBML import preserves UTF-8 non-ASCII chars in names

Imports a minimal SBML L2V4 document containing U+2013 EN DASH and
U+03BC GREEK SMALL LETTER MU in reaction and species name attributes,
and asserts the resulting BioModel preserves the chars byte-for-byte
in getSbmlName().

Tagged Fast. Exercises both the File path (readSbmlDocument(File),
which used to read with Charset.defaultCharset()) and the InputStream
path. On a UTF-8-default JVM both paths look equivalent, but the test
documents expected behavior and catches regressions if either path
is changed back to platform-default decoding.

A complementary CI job that forks a Cp1252-default JVM is the
follow-up that demonstrates the fix matters cross-platform.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: jcschaff

vcell-core/src/test/java/org/vcell/sbml/SBMLImportCharsetTest.java

@@ -0,0 +1,110 @@
+package org.vcell.sbml;
+
+import cbit.util.xml.VCLogger;
+import cbit.util.xml.VCLoggerException;
+import cbit.vcell.biomodel.BioModel;
+import cbit.vcell.model.ReactionStep;
+import cbit.vcell.model.SpeciesContext;
+import org.junit.jupiter.api.Tag;
+import org.junit.jupiter.api.Test;
+import org.vcell.sbml.vcell.SBMLImporter;
+
+import java.io.File;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+/**
+ * Verifies SBML import reads non-ASCII attribute values byte-for-byte from a
+ * UTF-8 source. The two reaction-name patterns chosen here (en-dash U+2013 and
+ * Greek mu U+03BC) are common in scientific notation and would mojibake under
+ * the previous {@code Charset.defaultCharset()} read on a non-UTF-8 JVM.
+ */
+@Tag("Fast")
+public class SBMLImportCharsetTest {
+
+    private static class CapturingVCLogger extends VCLogger {
+        @Override public boolean hasMessages() { return false; }
+        @Override public void sendAllMessages() { }
+        @Override public void sendMessage(Priority p, ErrorType et, String message) throws VCLoggerException {
+            if (p == Priority.HighPriority) {
+                throw new VCLoggerException(p + " " + et + ": " + message);
+            }
+        }
+    }
+
+    private static final String SBML_WITH_NON_ASCII =
+            "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
+            "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" level=\"2\" version=\"4\">\n" +
+            "  <model id=\"charsetTestModel\">\n" +
+            "    <listOfCompartments>\n" +
+            "      <compartment id=\"c1\" size=\"1.0\"/>\n" +
+            "    </listOfCompartments>\n" +
+            "    <listOfSpecies>\n" +
+            "      <species id=\"s1\" name=\"μ-prot\" compartment=\"c1\" initialConcentration=\"1.0\"/>\n" +
+            "    </listOfSpecies>\n" +
+            "    <listOfReactions>\n" +
+            "      <reaction id=\"r1\" name=\"k_14–3–3\">\n" +
+            "        <listOfProducts>\n" +
+            "          <speciesReference species=\"s1\"/>\n" +
+            "        </listOfProducts>\n" +
+            "        <kineticLaw>\n" +
+            "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" +
+            "            <cn>1.0</cn>\n" +
+            "          </math>\n" +
+            "        </kineticLaw>\n" +
+            "      </reaction>\n" +
+            "    </listOfReactions>\n" +
+            "  </model>\n" +
+            "</sbml>\n";
+
+    @Test
+    public void importsUtf8ReactionAndSpeciesNames() throws Exception {
+        Path tmp = Files.createTempFile("vcell-charset-test-", ".xml");
+        try {
+            Files.write(tmp, SBML_WITH_NON_ASCII.getBytes(StandardCharsets.UTF_8));
+
+            SBMLImporter importer = new SBMLImporter(tmp.toAbsolutePath().toString(), new CapturingVCLogger(), false);
+            BioModel bioModel = importer.getBioModel();
+            assertNotNull(bioModel);
+
+            ReactionStep r1 = null;
+            for (ReactionStep rs : bioModel.getModel().getReactionSteps()) {
+                if ("r1".equals(rs.getName())) { r1 = rs; break; }
+            }
+            assertNotNull(r1, "expected reaction with id 'r1' in imported model");
+            assertEquals("k_14–3–3", r1.getSbmlName(),
+                    "reaction sbmlName must preserve U+2013 EN DASH characters");
+
+            SpeciesContext s1 = null;
+            for (SpeciesContext sc : bioModel.getModel().getSpeciesContexts()) {
+                if ("s1".equals(sc.getName())) { s1 = sc; break; }
+            }
+            assertNotNull(s1, "expected species with id 's1' in imported model");
+            assertEquals("μ-prot", s1.getSbmlName(),
+                    "species sbmlName must preserve U+03BC GREEK SMALL LETTER MU");
+        } finally {
+            Files.deleteIfExists(tmp);
+        }
+    }
+
+    @Test
+    public void inputStreamPathPreservesUtf8() throws Exception {
+        try (java.io.ByteArrayInputStream in =
+                     new java.io.ByteArrayInputStream(SBML_WITH_NON_ASCII.getBytes(StandardCharsets.UTF_8))) {
+            SBMLImporter importer = new SBMLImporter(in, new CapturingVCLogger(), false);
+            BioModel bioModel = importer.getBioModel();
+            assertNotNull(bioModel);
+
+            ReactionStep r1 = null;
+            for (ReactionStep rs : bioModel.getModel().getReactionSteps()) {
+                if ("r1".equals(rs.getName())) { r1 = rs; break; }
+            }
+            assertNotNull(r1);
+            assertEquals("k_14–3–3", r1.getSbmlName());
+        }
+    }
+}