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Fix BEAUti startup, duplicate version listing, and example packaging #98

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Merged
walterxie merged 1 commit into from
Jun 18, 2026
Merged

Fix BEAUti startup, duplicate version listing, and example packaging #98

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23 changes: 22 additions & 1 deletion beast-base/src/assembly/package.xml
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Expand Up @@ -4,9 +4,18 @@
<!-- Builds the installable BEAST.base package zip:
version.xml (the BEAST.base package descriptor, at repo root)
lib/beast-base.jar + its third-party runtime dependencies
examples/ example XML (+ nexus data) shown in BEAUti
beast-pkgmgmt is excluded: it is the bootstrap/launcher and is always
provided by the core distribution, so bundling it here would duplicate
the beast.pkgmgmt module on the module path. -->
the beast.pkgmgmt module on the module path.

Examples are shipped *inside the package* (not only in the release
bundle root) so that a BEAST.base point release can update them via the
package manager: seedBundledPackage()/the package manager extract them
to <user package dir>/BEAST.base/examples, which BeautiTabPane and
PackageHealthChecker discover by scanning getBeastDirectories(). The
curated subset mirrors what release/.../assemble-bundle.sh copies into
the bundle root. -->
<id>package</id>
<formats>
<format>zip</format>
Expand All @@ -20,6 +29,18 @@
</file>
</files>

<fileSets>
<fileSet>
<directory>${project.basedir}/src/test/resources/beast.base/examples</directory>
<outputDirectory>examples</outputDirectory>
<includes>
<include>*.xml</include>
<include>spec/*.xml</include>
<include>nexus/**</include>
</includes>
</fileSet>
</fileSets>

<dependencySets>
<dependencySet>
<outputDirectory>lib</outputDirectory>
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17 changes: 14 additions & 3 deletions beast-base/src/main/java/beast/base/minimal/BeastMain.java
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Expand Up @@ -69,6 +69,12 @@ public static void printUsage(final Arguments arguments) {
private static void printVersion() {
Log.info("BEAST " + (new BEASTVersion()).getVersionString());
Log.info("---");
// The same package can be discovered through more than one directory on
// the package path (e.g. BEAST.base is found both in the user package dir
// and via the bundle-root version.xml). List each package once, noting
// where it was found; later duplicates are reported as skipped, but only
// in verbose mode.
java.util.Set<String> printed = new java.util.HashSet<>();
for (String jarDirName : PackageManager.getBeastDirectories()) {
File versionFile = new File(jarDirName + "/version.xml");
if (versionFile.exists()) {
Expand All @@ -77,9 +83,14 @@ private static void printVersion() {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
Document doc = factory.newDocumentBuilder().parse(versionFile);
Element packageElement = doc.getDocumentElement();
Log.info.print(packageElement.getAttribute("name") + " v" + packageElement.getAttribute("version"));
Log.debug.print(" " + jarDirName);
Log.info.print("\n");
String nameAndVersion = packageElement.getAttribute("name") + " v" + packageElement.getAttribute("version");
if (printed.add(nameAndVersion)) {
Log.info.print(nameAndVersion);
Log.debug.print(" (found in " + jarDirName + ")");
Log.info.print("\n");
} else {
Log.debug.println("Skipping duplicate " + nameAndVersion + " found in " + jarDirName);
}
} catch (IOException| SAXException| ParserConfigurationException e) {
Log.err(e.getMessage());
}
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17 changes: 14 additions & 3 deletions beast-fx/src/main/java/beastfx/app/beast/BeastMain.java
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Expand Up @@ -103,6 +103,12 @@ public static void printUsage(final Arguments arguments) {
private static void printVersion() {
Log.info("BEAST " + (new BEASTVersion()).getVersionString());
Log.info("---");
// The same package can be discovered through more than one directory on
// the package path (e.g. BEAST.base is found both in the user package dir
// and via the bundle-root version.xml). List each package once, noting
// where it was found; later duplicates are reported as skipped, but only
// in verbose mode.
java.util.Set<String> printed = new java.util.HashSet<>();
for (String jarDirName : PackageManager.getBeastDirectories()) {
File versionFile = new File(jarDirName + "/version.xml");
if (versionFile.exists()) {
Expand All @@ -111,9 +117,14 @@ private static void printVersion() {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
Document doc = factory.newDocumentBuilder().parse(versionFile);
Element packageElement = doc.getDocumentElement();
Log.info.print(packageElement.getAttribute("name") + " v" + packageElement.getAttribute("version"));
Log.debug.print(" " + jarDirName);
Log.info.print("\n");
String nameAndVersion = packageElement.getAttribute("name") + " v" + packageElement.getAttribute("version");
if (printed.add(nameAndVersion)) {
Log.info.print(nameAndVersion);
Log.debug.print(" (found in " + jarDirName + ")");
Log.info.print("\n");
} else {
Log.debug.println("Skipping duplicate " + nameAndVersion + " found in " + jarDirName);
}
} catch (IOException| SAXException| ParserConfigurationException e) {
Log.err(e.getMessage());
}
Expand Down
31 changes: 30 additions & 1 deletion beast-pkgmgmt/src/main/java/beast/pkgmgmt/BEASTClassLoader.java
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Expand Up @@ -76,6 +76,14 @@ public static Class<?> forName(String className) throws ClassNotFoundException {
ClassLoader loader = class2loaderMap.get(className);
try {
return Class.forName(className, false, loader);
} catch (ClassNotFoundException e) {
// The mapped loader cannot see this class. This happens when the
// provider was registered from a version.xml scan (via
// resolveLoaderFor → fallback system/context loader) before the
// owning package's plugin ModuleLayer was registered: the later
// putIfAbsent in registerPluginLayer() then cannot replace the
// stale fallback loader. Fall through to search the plugin layers
// and correct the mapping below.
} catch (NoClassDefFoundError e) {
String missing = e.getMessage();
if (missing != null && (missing.startsWith("beastfx/") || missing.startsWith("beastfx.")
Expand All @@ -91,8 +99,15 @@ public static Class<?> forName(String className) throws ClassNotFoundException {
// 2. Plugin layers (external BEAST packages)
for (ModuleLayer layer : pluginLayers) {
for (Module module : layer.modules()) {
ClassLoader mcl = module.getClassLoader();
if (mcl == null) continue;
try {
return Class.forName(className, false, module.getClassLoader());
Class<?> c = Class.forName(className, false, mcl);
// Self-heal: cache the loader that actually resolved the
// class so subsequent lookups skip the failing mapped loader
// (and the exception-driven fall-through above).
class2loaderMap.put(className, mcl);
return c;
} catch (ClassNotFoundException | NoClassDefFoundError e) {
// try next module
}
Expand Down Expand Up @@ -559,6 +574,20 @@ private static ClassLoader resolveLoaderFor(String provider) {
if (loader != null) return loader;
}
}
// Also consult already-registered plugin layers: a package's classes
// live in its own plugin ModuleLayer (e.g. beast.fx for the BEAUti
// input editors), not in the boot layer. Without this, providers listed
// in a version.xml would be mapped to the fallback system loader, which
// cannot load them, leaving forName() to fall through on every lookup.
for (ModuleLayer layer : pluginLayers) {
for (Module m : layer.modules()) {
java.lang.module.ModuleDescriptor desc = m.getDescriptor();
if (desc != null && desc.packages().contains(pkg)) {
ClassLoader loader = m.getClassLoader();
if (loader != null) return loader;
}
}
}
return fallbackClassLoader();
}
}
44 changes: 44 additions & 0 deletions beast-pkgmgmt/src/test/java/beast/pkgmgmt/ModuleLayerCrossDependencyTest.java
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Expand Up @@ -9,12 +9,15 @@
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.jar.JarEntry;
import java.util.jar.JarOutputStream;
import java.util.spi.ToolProvider;
import java.util.stream.Stream;

import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;

/**
Expand Down Expand Up @@ -64,6 +67,47 @@ public void dependentPackageResolvesAgainstAnotherPluginLayer() throws Exception
assertEquals("base+plugin", result, "cross-layer call should execute");
}

/**
* Regression test for the BEAUti "ClassNotFoundException: beastfx.app.inputeditor.*"
* failure. A package's service providers are listed in its version.xml. If a
* version.xml scan registers a provider (via addServices → resolveLoaderFor)
* before the owning package's plugin ModuleLayer is registered, the provider
* is mapped to the fallback system loader, which cannot load it. registerPluginLayer()
* uses putIfAbsent and so cannot replace that stale mapping. forName() must still
* resolve the class by falling through to the plugin layers.
*/
@Test
public void forNameHealsStaleFallbackLoaderMapping() throws Exception {
ToolProvider javac = ToolProvider.findFirst("javac").orElse(null);
Assumptions.assumeTrue(javac != null, "no javac tool available - skipping");

Path work = Files.createTempDirectory("stale-loader-test");

// A modular jar exporting a provider class, mimicking beast.fx's input editors.
Path editorJar = buildModuleJar(javac, work, "fxstaletest", null,
"module fxstaletest { exports fxstaletest; }",
"fxstaletest", "Editor",
"package fxstaletest; public class Editor { }");

// 1. Simulate the version.xml scan that runs before the plugin layer exists:
// the provider is mapped to the fallback system loader (cannot load it).
Map<String, Set<String>> services = Map.of(
"fxstaletest.InputEditor", Set.of("fxstaletest.Editor"));
BEASTClassLoader.classLoader.addServices("FxStaleTest", services);

// 2. Register the package's real plugin layer. putIfAbsent leaves the
// stale fallback mapping from step 1 in place.
boolean loaded = PackageManager.createAndRegisterModuleLayer(
List.of(editorJar), null, "FxStaleTest", "1.0", "FxStaleTest");
assertTrue(loaded, "provider module should load into a plugin layer");

// 3. Despite the stale mapping, forName must resolve the class via the
// plugin layer (previously threw ClassNotFoundException here).
Class<?> editor = BEASTClassLoader.forName("fxstaletest.Editor");
assertNotNull(editor);
assertEquals("fxstaletest.Editor", editor.getName());
}

/** Compile a single-package module and pack it into a jar; return the jar path. */
private static Path buildModuleJar(ToolProvider javac, Path work, String moduleName,
Path modulePathJar, String moduleInfo,
Expand Down
21 changes: 10 additions & 11 deletions release/Linux/assemble-bundle.sh
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Expand Up @@ -152,20 +152,19 @@ else
echo " WARNING: DensiTree.jar not found — densitree script will not work"
fi

# ── Step 6: Copy examples ─────────────────────────────────────────────────────
# ── Step 6: Extract examples from the BEAST.base package zip ──────────────────
# The bundle-root examples/ are extracted from the same package zip seeded into
# the user dir (lib/packages/), so the example set has a single source of truth
# (beast-base/src/assembly/package.xml) and the bundle-root and packaged copies
# cannot drift. The bundle-root copy is kept so `beast -validate examples/...`
# works from the install dir before first-run seeding.
echo ""
echo "==> Step 6: Copying examples..."
EXAMPLES_DIR="$REPO_ROOT/beast-base/src/test/resources/beast.base/examples"
if [ -d "$EXAMPLES_DIR" ]; then
find "$EXAMPLES_DIR" -maxdepth 1 -name "*.xml" -exec cp {} "$BUNDLE/examples/" \;
mkdir -p "$BUNDLE/examples/spec"
[ -d "$EXAMPLES_DIR/spec" ] && \
find "$EXAMPLES_DIR/spec" -maxdepth 1 -name "*.xml" -exec cp {} "$BUNDLE/examples/spec/" \;
[ -d "$EXAMPLES_DIR/nexus" ] && cp -r "$EXAMPLES_DIR/nexus" "$BUNDLE/examples/"
echo "==> Step 6: Extracting examples from $(basename "$BASE_PKG_ZIP")..."
if unzip -o -q "$BASE_PKG_ZIP" 'examples/*' -d "$BUNDLE"; then
EXAMPLE_COUNT=$(find "$BUNDLE/examples" -name "*.xml" | wc -l | tr -d ' ')
echo " Copied ${EXAMPLE_COUNT} example XML files (incl. spec/)"
echo " Extracted ${EXAMPLE_COUNT} example XML files (incl. spec/)"
else
echo " WARNING: examples not found at $EXAMPLES_DIR"
echo " WARNING: no examples found in $BASE_PKG_ZIP"
fi

# ── Step 7: Copy version.xml and docs ────────────────────────────────────────
Expand Down
22 changes: 8 additions & 14 deletions release/Mac/build-sign-dmg.sh
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Expand Up @@ -558,21 +558,15 @@ else
fi

# ── examples/ — example BEAST XML files ──────────────────────────────────────
EXAMPLES_DIR="$REPO_ROOT/beast-base/src/test/resources/beast.base/examples"
if [ -d "$EXAMPLES_DIR" ]; then
echo " Copying examples/..."
mkdir -p "$OUTPUT/examples"
# Copy top-level XML files
find "$EXAMPLES_DIR" -maxdepth 1 -name "*.xml" -exec cp {} "$OUTPUT/examples/" \;
# Copy nexus subdirectory
if [ -d "$EXAMPLES_DIR/nexus" ]; then
cp -r "$EXAMPLES_DIR/nexus" "$OUTPUT/examples/nexus"
fi
if [ -d "$EXAMPLES_DIR/spec" ]; then
cp -r "$EXAMPLES_DIR/spec" "$OUTPUT/examples/spec"
fi
# Extracted from the BEAST.base package zip seeded into the user dir
# (Contents/app/packages/), so the example set has a single source of truth
# (beast-base/src/assembly/package.xml) and the bundle-root and packaged copies
# cannot drift. The bundle-root copy is kept so `beast -validate examples/...`
# works from the install dir before first-run seeding.
if [ -n "$BASE_PKG_ZIP" ] && unzip -o -q "$BASE_PKG_ZIP" 'examples/*' -d "$OUTPUT"; then
echo " Extracted examples/ from $(basename "$BASE_PKG_ZIP")"
else
echo " WARNING: $EXAMPLES_DIR not found — skipping examples/"
echo " WARNING: no examples found in BEAST.base package zip — skipping examples/"
fi

# ── README and LICENSE ─────────────────────────────────────────────────────
Expand Down
21 changes: 10 additions & 11 deletions release/Windows/assemble-bundle.sh
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Expand Up @@ -244,20 +244,19 @@ WINBIN_DIR="$SCRIPT_DIR/bat"
mkdir -p "$BUNDLE/bat"
cp "$WINBIN_DIR/"*.bat "$BUNDLE/bat/"

# ── Step 7: Copy examples ─────────────────────────────────────────────────────
# ── Step 7: Extract examples from the BEAST.base package zip ──────────────────
# The bundle-root examples/ are extracted from the same package zip seeded into
# the user dir (app/packages/), so the example set has a single source of truth
# (beast-base/src/assembly/package.xml) and the bundle-root and packaged copies
# cannot drift. The bundle-root copy is kept so `beast -validate examples/...`
# works from the install dir before first-run seeding.
echo ""
echo "==> Step 7: Copying examples..."
EXAMPLES_DIR="$REPO_ROOT/beast-base/src/test/resources/beast.base/examples"
if [ -d "$EXAMPLES_DIR" ]; then
mkdir -p "$BUNDLE/examples/spec"
find "$EXAMPLES_DIR" -maxdepth 1 -name "*.xml" -exec cp {} "$BUNDLE/examples/" \;
[ -d "$EXAMPLES_DIR/spec" ] && \
find "$EXAMPLES_DIR/spec" -maxdepth 1 -name "*.xml" -exec cp {} "$BUNDLE/examples/spec/" \;
[ -d "$EXAMPLES_DIR/nexus" ] && cp -r "$EXAMPLES_DIR/nexus" "$BUNDLE/examples/"
echo "==> Step 7: Extracting examples from $(basename "$BASE_PKG_ZIP")..."
if unzip -o -q "$BASE_PKG_ZIP" 'examples/*' -d "$BUNDLE"; then
EXAMPLE_COUNT=$(find "$BUNDLE/examples" -name "*.xml" | wc -l | tr -d ' ')
echo " Copied ${EXAMPLE_COUNT} example XML files (incl. spec/)"
echo " Extracted ${EXAMPLE_COUNT} example XML files (incl. spec/)"
else
echo " WARNING: examples not found at $EXAMPLES_DIR"
echo " WARNING: no examples found in $BASE_PKG_ZIP"
fi

# ── Step 8: Copy version.xml and docs ────────────────────────────────────────
Expand Down