From ba18dcfa2662eb3f7c1d9a0263055cee47ab4210 Mon Sep 17 00:00:00 2001 From: Remco Bouckaert Date: Wed, 14 Mar 2018 12:55:42 +1300 Subject: [PATCH] rename AddOnManager to PackageManager #40 --- build.xml | 5 +- .../bin/{addonmanager => packagemanager} | 2 +- .../jrebin/{addonmanager => packagemanager} | 2 +- src/beast/app/BeastMCMC.java | 6 +- src/beast/app/DocMaker.java | 6 +- src/beast/app/ModelBuilder.java | 4 +- src/beast/app/beastapp/BeastLauncher.java | 33 +++-- src/beast/app/beauti/Beauti.java | 22 ++-- .../app/beauti/BeautiAlignmentProvider.java | 4 +- src/beast/app/beauti/BeautiDoc.java | 4 +- src/beast/app/beauti/JPackageDialog.java | 16 +-- .../app/beauti/JPackageRepositoryDialog.java | 8 +- .../app/beauti/PriorListInputEditor.java | 4 +- src/beast/app/beauti/PriorProvider.java | 4 + .../app/draw/BEASTObjectInputEditor.java | 4 +- src/beast/app/draw/BEASTObjectPanel.java | 1 + src/beast/app/draw/Document.java | 4 +- src/beast/app/draw/InputEditorFactory.java | 6 +- src/beast/app/draw/ModelBuilder.java | 4 +- src/beast/app/tools/AppLauncher.java | 27 ++-- src/beast/app/util/Utils.java | 7 +- src/beast/evolution/alignment/Alignment.java | 6 +- src/beast/util/JSONParser.java | 2 +- src/beast/util/Package.java | 4 +- src/beast/util/PackageDependency.java | 2 +- ...{AddOnManager.java => PackageManager.java} | 119 ++++++++++-------- src/beast/util/XMLParser.java | 4 +- src/beast/util/XMLParserUtils.java | 2 +- src/beast/util/XMLProducer.java | 2 +- .../beast/integration/DocumentationTest.java | 6 +- src/test/beast/integration/InputTypeTest.java | 10 +- .../beast/integration/XMLElementNameTest.java | 6 +- version.xml | 2 +- 33 files changed, 174 insertions(+), 164 deletions(-) rename release/Linux/bin/{addonmanager => packagemanager} (90%) rename release/Linux/jrebin/{addonmanager => packagemanager} (90%) rename src/beast/util/{AddOnManager.java => PackageManager.java} (95%) diff --git a/build.xml b/build.xml index 66532834c..f6c69d39e 100644 --- a/build.xml +++ b/build.xml @@ -93,7 +93,6 @@ - @@ -114,7 +113,6 @@ - @@ -157,7 +155,6 @@ - @@ -179,7 +176,7 @@ - + diff --git a/release/Linux/bin/addonmanager b/release/Linux/bin/packagemanager similarity index 90% rename from release/Linux/bin/addonmanager rename to release/Linux/bin/packagemanager index ba67577dd..5329e3534 100755 --- a/release/Linux/bin/addonmanager +++ b/release/Linux/bin/packagemanager @@ -29,5 +29,5 @@ if [ -z "$JAVA_HOME" ]; then else JAVA=$JAVA_HOME/bin/java fi -$JAVA -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.AddOnManager $* +$JAVA -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.PackageManager $* diff --git a/release/Linux/jrebin/addonmanager b/release/Linux/jrebin/packagemanager similarity index 90% rename from release/Linux/jrebin/addonmanager rename to release/Linux/jrebin/packagemanager index a069e10ed..d14c683ae 100755 --- a/release/Linux/jrebin/addonmanager +++ b/release/Linux/jrebin/packagemanager @@ -30,5 +30,5 @@ if [ -z "$JAVA_HOME" ]; then else JAVA=$JAVA_HOME/bin/java fi -$JAVA -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.AddOnManager $* +$JAVA -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/beast.jar" beast.util.PackageManager $* diff --git a/src/beast/app/BeastMCMC.java b/src/beast/app/BeastMCMC.java index 119493632..4e94a6e71 100644 --- a/src/beast/app/BeastMCMC.java +++ b/src/beast/app/BeastMCMC.java @@ -72,7 +72,7 @@ import beast.core.Logger; import beast.core.Runnable; import beast.core.util.Log; -import beast.util.AddOnManager; +import beast.util.PackageManager; import beast.util.JSONParser; import beast.util.JSONParserException; import beast.util.Randomizer; @@ -295,10 +295,10 @@ public void parseArgs(String[] args) throws IOException, XMLParserException, JSO start += 10; int end = str.indexOf(c, start); String packages = str.substring(start, end); - AddOnManager.loadExternalJars(packages); + PackageManager.loadExternalJars(packages); } } else { - AddOnManager.loadExternalJars(); + PackageManager.loadExternalJars(); } diff --git a/src/beast/app/DocMaker.java b/src/beast/app/DocMaker.java index ed25980bc..79931b15e 100644 --- a/src/beast/app/DocMaker.java +++ b/src/beast/app/DocMaker.java @@ -49,7 +49,7 @@ import beast.core.Input; import beast.core.Loggable; import beast.core.util.Log; -import beast.util.AddOnManager; +import beast.util.PackageManager; @@ -102,7 +102,7 @@ public DocMaker(String[] args) { public DocMaker() { // find plug ins to document - m_beastObjectNames = AddOnManager.find(beast.core.BEASTObject.class, AddOnManager.IMPLEMENTATION_DIR); + m_beastObjectNames = PackageManager.find(beast.core.BEASTObject.class, PackageManager.IMPLEMENTATION_DIR); /** determine hierarchical relation between plug-ins **/ m_isa = new HashMap<>(); m_ancestors = new HashMap<>(); @@ -570,7 +570,7 @@ public void generateDocs() throws FileNotFoundException { public static void main(String[] args) { try { System.err.println("Producing documentation..."); - AddOnManager.loadExternalJars(); + PackageManager.loadExternalJars(); DocMaker b = new DocMaker(args); b.generateDocs(); System.err.println("Done!!!"); diff --git a/src/beast/app/ModelBuilder.java b/src/beast/app/ModelBuilder.java index 5035be83e..1c2b0b56d 100644 --- a/src/beast/app/ModelBuilder.java +++ b/src/beast/app/ModelBuilder.java @@ -35,7 +35,7 @@ import javax.swing.JPanel; import javax.swing.UIManager; -import beast.util.AddOnManager; +import beast.util.PackageManager; import beast.util.Randomizer; @@ -55,7 +55,7 @@ public class ModelBuilder extends JPanel { public static void main(String args[]) { Randomizer.setSeed(127); try { - AddOnManager.loadExternalJars(); + PackageManager.loadExternalJars(); } catch (Exception e) { e.printStackTrace();// ignore } diff --git a/src/beast/app/beastapp/BeastLauncher.java b/src/beast/app/beastapp/BeastLauncher.java index 62a19dc82..9ae2b4e7a 100644 --- a/src/beast/app/beastapp/BeastLauncher.java +++ b/src/beast/app/beastapp/BeastLauncher.java @@ -10,7 +10,6 @@ import java.io.InputStream; import java.io.InputStreamReader; import java.io.OutputStream; -import java.io.PrintStream; import java.io.UnsupportedEncodingException; import java.lang.reflect.InvocationTargetException; import java.net.URL; @@ -33,7 +32,7 @@ import beast.app.BEASTVersion; import beast.app.util.Utils6; import beast.core.util.Log; -import beast.util.AddOnManager; +import beast.util.PackageManager; import beast.util.Package; import beast.util.PackageVersion; @@ -144,7 +143,7 @@ private static void createBeastPackage(File jarDir0) { File target = new File(dir + pathDelimiter + "beast.jar"); copyFileUsingStream(beastJar, target); - String version = "\n" + ""; + String version = "\n" + ""; FileWriter outfile = new FileWriter(userDir + pathDelimiter + "BEAST" + pathDelimiter + "version.xml"); outfile.write(version); outfile.close(); @@ -338,7 +337,7 @@ private static double parseVersion(String versionString) { protected static String getPath(boolean useStrictVersions, String beastFile) throws NoSuchMethodException, SecurityException, ClassNotFoundException, IllegalAccessException, IllegalArgumentException, InvocationTargetException, IOException { installBEASTPackage(); - AddOnManager.initialise(); + PackageManager.initialise(); if (useStrictVersions) { @@ -380,7 +379,7 @@ protected static String getPath(boolean useStrictVersions, String beastFile) thr } } - AddOnManager.checkInstalledDependencies(); + PackageManager.checkInstalledDependencies(); // just load all packages StringBuilder buf = new StringBuilder(); @@ -400,13 +399,13 @@ protected static String getPath(boolean useStrictVersions, String beastFile) thr private static String determinePackagePath(String packagesString) throws UnsupportedEncodingException { StringBuilder buf = new StringBuilder(); - if (AddOnManager.getBEASTInstallDir() != null) { + if (PackageManager.getBEASTInstallDir() != null) { buf.append(File.pathSeparator); - buf.append(URLDecoder.decode(AddOnManager.getBEASTInstallDir() + "/lib/beast.jar", "UTF-8")); + buf.append(URLDecoder.decode(PackageManager.getBEASTInstallDir() + "/lib/beast.jar", "UTF-8")); } if (packagesString != null && packagesString.trim().length() > 0) { Map packages = new HashMap(); - AddOnManager.addInstalledPackages(packages); + PackageManager.addInstalledPackages(packages); String unavailablePackages = ""; String [] packageAndVersions = packagesString.split(":"); @@ -419,8 +418,8 @@ private static String determinePackagePath(String packagesString) throws Unsuppo String pkgversion = s.substring(i+1).trim().replaceAll("v", ""); Package pkg = new Package(pkgname); PackageVersion version = new PackageVersion(pkgversion); - AddOnManager.useArchive(true); - String dirName = AddOnManager.getPackageDir(pkg, version, false, System.getProperty("BEAST_ADDON_PATH")); + PackageManager.useArchive(true); + String dirName = PackageManager.getPackageDir(pkg, version, false, PackageManager.getBeastPacakgePathProperty()); if (new File(dirName).exists()) { buf.append(addJarsToPath(dirName, classes)); } else { @@ -429,8 +428,8 @@ private static String determinePackagePath(String packagesString) throws Unsuppo if (pkg2 == null || !pkg2.isInstalled() || !pkg2.getInstalledVersion().equals(version)) { unavailablePackages += s +", "; } else { - AddOnManager.useArchive(false); - dirName = AddOnManager.getPackageDir(pkg, version, false, System.getProperty("BEAST_ADDON_PATH")); + PackageManager.useArchive(false); + dirName = PackageManager.getPackageDir(pkg, version, false, PackageManager.getBeastPacakgePathProperty()); if (new File(dirName).exists()) { buf.append(addJarsToPath(dirName, classes)); } else { @@ -456,12 +455,12 @@ private static String determinePackagePath(String packagesString) throws Unsuppo private static String determinePackagePath() throws UnsupportedEncodingException { StringBuilder buf = new StringBuilder(); - if (AddOnManager.getBEASTInstallDir() != null) { + if (PackageManager.getBEASTInstallDir() != null) { buf.append(File.pathSeparator); - buf.append(URLDecoder.decode(AddOnManager.getBEASTInstallDir() + "/lib/beast.jar", "UTF-8")); + buf.append(URLDecoder.decode(PackageManager.getBEASTInstallDir() + "/lib/beast.jar", "UTF-8")); } Set classes = new HashSet(); - for (String jarDirName : AddOnManager.getBeastDirectories()) { + for (String jarDirName : PackageManager.getBeastDirectories()) { try { File versionFile = new File(jarDirName + "/version.xml"); String packageNameAndVersion = null; @@ -470,8 +469,8 @@ private static String determinePackagePath() throws UnsupportedEncodingException // print name and version of package DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); Document doc = factory.newDocumentBuilder().parse(versionFile); - Element addon = doc.getDocumentElement(); - packageNameAndVersion = addon.getAttribute("name") + " v" + addon.getAttribute("version"); + Element packageElement = doc.getDocumentElement(); + packageNameAndVersion = packageElement.getAttribute("name") + " v" + packageElement.getAttribute("version"); // Log.warning.println("Loading package " + // packageNameAndVersion); // Utils.logToSplashScreen("Loading package " + diff --git a/src/beast/app/beauti/Beauti.java b/src/beast/app/beauti/Beauti.java index f4645a1e1..7c9b7aab5 100644 --- a/src/beast/app/beauti/Beauti.java +++ b/src/beast/app/beauti/Beauti.java @@ -66,7 +66,7 @@ import beast.core.util.Log; import beast.evolution.alignment.Alignment; import beast.math.distributions.MRCAPrior; -import beast.util.AddOnManager; +import beast.util.PackageManager; import jam.framework.DocumentFrame; @@ -171,7 +171,7 @@ int tabNrForPanel(int panelNr) { Action a_new = new ActionNew(); public Action a_load = new ActionLoad(); Action a_template = new ActionTemplate(); - Action a_addOn = new ActionAddOn(); + Action a_managePackages = new ActionManagePacakges(); Action a_appLauncher = new ActionAppLauncher(); // public Action a_import = new ActionImport(); public Action a_save = new ActionSave(); @@ -403,10 +403,10 @@ public void actionPerformed(ActionEvent ae) { } // actionPerformed } // ActionTemplate - class ActionAddOn extends MyAction { + class ActionManagePacakges extends MyAction { private static final long serialVersionUID = 1; - public ActionAddOn() { + public ActionManagePacakges() { super("Manage Packages", "Manage Packages", "package", -1); } // c'tor @@ -820,7 +820,7 @@ private void createFileMenu() { } templateMenu.addSeparator(); templateMenu.add(a_template); - fileMenu.add(a_addOn); + fileMenu.add(a_managePackages); fileMenu.add(a_appLauncher); fileMenu.addSeparator(); fileMenu.add(a_save); @@ -1001,7 +1001,7 @@ public void actionPerformed(ActionEvent e) { private List getTemplateActions() { List actions = new ArrayList<>(); - List beastDirectories = AddOnManager.getBeastDirectories(); + List beastDirectories = PackageManager.getBeastDirectories(); for (String dirName : beastDirectories) { File dir = new File(dirName + "/templates"); getTemplateActionForDir(dir, actions); @@ -1042,7 +1042,7 @@ private void getTemplateActionForDir(File dir, List actions) { private List getWorkDirActions() { List actions = new ArrayList<>(); - List beastDirectories = AddOnManager.getBeastDirectories(); + List beastDirectories = PackageManager.getBeastDirectories(); Set doneDirs = new HashSet<>(); for (String dir : beastDirectories) { if (!doneDirs.contains(dir)) { @@ -1220,7 +1220,7 @@ public void close() throws IOException { } } - AddOnManager.loadExternalJars(); + PackageManager.loadExternalJars(); //if (!Utils.isMac()) { Utils.loadUIManager(); //} @@ -1412,10 +1412,10 @@ public static void main(String[] args) { public void run() { String statuString = Utils.getBeautiProperty("package.update.status"); if (statuString == null) { - statuString = AddOnManager.UpdateStatus.AUTO_CHECK_AND_ASK.toString(); + statuString = PackageManager.UpdateStatus.AUTO_CHECK_AND_ASK.toString(); } - AddOnManager.UpdateStatus updateStatus = AddOnManager.UpdateStatus.valueOf(statuString); - AddOnManager.updatePackages(updateStatus, true); + PackageManager.UpdateStatus updateStatus = PackageManager.UpdateStatus.valueOf(statuString); + PackageManager.updatePackages(updateStatus, true); }; }.start(); } diff --git a/src/beast/app/beauti/BeautiAlignmentProvider.java b/src/beast/app/beauti/BeautiAlignmentProvider.java index 9dcada2be..714f18ce9 100644 --- a/src/beast/app/beauti/BeautiAlignmentProvider.java +++ b/src/beast/app/beauti/BeautiAlignmentProvider.java @@ -38,7 +38,7 @@ import beast.evolution.alignment.Sequence; import beast.evolution.datatype.DataType; import beast.math.distributions.MRCAPrior; -import beast.util.AddOnManager; +import beast.util.PackageManager; import beast.util.NexusParser; import beast.util.XMLParser; @@ -60,7 +60,7 @@ private void initImporters() { importers.add(new FastaImporter()); // build up list of data types - List importerClasses = AddOnManager.find(AlignmentImporter.class, IMPLEMENTATION_DIR); + List importerClasses = PackageManager.find(AlignmentImporter.class, IMPLEMENTATION_DIR); for (String _class: importerClasses) { try { if (!_class.startsWith(this.getClass().getName())) { diff --git a/src/beast/app/beauti/BeautiDoc.java b/src/beast/app/beauti/BeautiDoc.java index f40133904..e1a688912 100644 --- a/src/beast/app/beauti/BeautiDoc.java +++ b/src/beast/app/beauti/BeautiDoc.java @@ -483,7 +483,7 @@ void initialize(ActionOnExit endState, String xml, String template, String fileN public String processTemplate(String fileName) throws IOException { final String MERGE_ELEMENT = "mergepoint"; // first gather the set of potential directories with templates - Set dirs = new HashSet<>();// AddOnManager.getBeastDirectories(); + Set dirs = new HashSet<>(); String pathSep = System.getProperty("path.separator"); String classpath = System.getProperty("java.class.path"); String fileSep = System.getProperty("file.separator"); @@ -536,7 +536,7 @@ public String processTemplate(String fileName) throws IOException { // find XML to merge // ensure processed templates are unique in name. // This prevents loading templates twice, once from the development area - // and once from .beast2-addon area + // and once from .beast2-package area Set loadedTemplates = new HashSet<>(); for (String dirName : dirs) { Log.info.println("Investigating " + dirName); diff --git a/src/beast/app/beauti/JPackageDialog.java b/src/beast/app/beauti/JPackageDialog.java index 6394b7a8e..2cdccec50 100644 --- a/src/beast/app/beauti/JPackageDialog.java +++ b/src/beast/app/beauti/JPackageDialog.java @@ -3,7 +3,7 @@ import beast.app.util.Arguments; import beast.app.util.Utils; import beast.core.Description; -import beast.util.AddOnManager; +import beast.util.PackageManager; import beast.util.Package; import beast.util.PackageVersion; @@ -25,7 +25,7 @@ import java.util.List; import java.util.stream.Collectors; -import static beast.util.AddOnManager.*; +import static beast.util.PackageManager.*; /** * dialog for managing Package. @@ -45,13 +45,13 @@ public class JPackageDialog extends JPanel { boolean useLatestVersion = true; TreeMap packageMap = new TreeMap<>((s1,s2)->{ - if (s1.equals(AddOnManager.BEAST_PACKAGE_NAME)) { - if (s2.equals(AddOnManager.BEAST_PACKAGE_NAME)) { + if (s1.equals(PackageManager.BEAST_PACKAGE_NAME)) { + if (s2.equals(PackageManager.BEAST_PACKAGE_NAME)) { return 0; } return -1; } - if (s2.equals(AddOnManager.BEAST_PACKAGE_NAME)) { + if (s2.equals(PackageManager.BEAST_PACKAGE_NAME)) { return 1; } return s1.compareToIgnoreCase(s2); @@ -88,7 +88,7 @@ public void run() { if (isRunning) { t.interrupt(); JOptionPane.showMessageDialog(frame, "Download of file " + - AddOnManager.PACKAGES_XML + " timed out.
" + + PackageManager.PACKAGES_XML + " timed out.
" + "Perhaps this is due to lack of internet access
" + "or some security settings not allowing internet access." ); @@ -201,7 +201,7 @@ private void resetPackages() { if (!pkg.getName().equals("beast2")) packageList.add(pkg); - } catch (AddOnManager.PackageListRetrievalException e) { + } catch (PackageManager.PackageListRetrievalException e) { StringBuilder msgBuilder = new StringBuilder("" + e.getMessage() + "
"); if (e.getCause() instanceof IOException) msgBuilder.append(NO_CONNECTION_MESSAGE.replaceAll("\\.", ".
")); @@ -258,7 +258,7 @@ private Box createButtonBox() { setCursor(new Cursor(Cursor.WAIT_CURSOR)); Map packagesToInstall = new HashMap<>(); - AddOnManager.useArchive(!useLatestVersion); + PackageManager.useArchive(!useLatestVersion); for (int selRow : selectedRows) { Package selPackage = getSelectedPackage(selRow); if (selPackage != null) { diff --git a/src/beast/app/beauti/JPackageRepositoryDialog.java b/src/beast/app/beauti/JPackageRepositoryDialog.java index 1a5ee0558..8a23729ac 100644 --- a/src/beast/app/beauti/JPackageRepositoryDialog.java +++ b/src/beast/app/beauti/JPackageRepositoryDialog.java @@ -31,7 +31,7 @@ import javax.swing.*; import javax.swing.table.AbstractTableModel; -import beast.util.AddOnManager; +import beast.util.PackageManager; /** * @author Tim Vaughan @@ -49,11 +49,11 @@ public JPackageRepositoryDialog(final JFrame frame) { // Get current list of URLs: List urls; try { - urls = AddOnManager.getRepositoryURLs(); + urls = PackageManager.getRepositoryURLs(); } catch (MalformedURLException exception) { urls = new ArrayList<>(); try { - urls.add(new URL(AddOnManager.PACKAGES_XML)); + urls.add(new URL(PackageManager.PACKAGES_XML)); } catch (MalformedURLException e) { // Hard-coded URL is broken. Should never happen! e.printStackTrace(); @@ -127,7 +127,7 @@ public JPackageRepositoryDialog(final JFrame frame) { // DONE JButton OKButton = new JButton("Done"); OKButton.addActionListener(e -> { - AddOnManager.saveRepositoryURLs(repoTableModel.urls); + PackageManager.saveRepositoryURLs(repoTableModel.urls); setVisible(false); }); box.add(OKButton); diff --git a/src/beast/app/beauti/PriorListInputEditor.java b/src/beast/app/beauti/PriorListInputEditor.java index efc400beb..867ba1468 100644 --- a/src/beast/app/beauti/PriorListInputEditor.java +++ b/src/beast/app/beauti/PriorListInputEditor.java @@ -36,7 +36,7 @@ import beast.math.distributions.MRCAPrior; import beast.math.distributions.OneOnX; import beast.math.distributions.Prior; -import beast.util.AddOnManager; +import beast.util.PackageManager; @@ -225,7 +225,7 @@ private void initProviders() { priorProviders.add(new MRCAPriorProvider()); // build up list of data types - List importerClasses = AddOnManager.find(PriorProvider.class, new String[]{"beast.app"}); + List importerClasses = PackageManager.find(PriorProvider.class, new String[]{"beast.app"}); for (String _class: importerClasses) { try { if (!_class.startsWith(this.getClass().getName())) { diff --git a/src/beast/app/beauti/PriorProvider.java b/src/beast/app/beauti/PriorProvider.java index d824303ad..7924574ea 100644 --- a/src/beast/app/beauti/PriorProvider.java +++ b/src/beast/app/beauti/PriorProvider.java @@ -19,6 +19,10 @@ public interface PriorProvider { */ public List createDistribution(BeautiDoc doc); + default public List createDistribution(BeautiDoc doc, List args) { + return createDistribution(doc); + } + /** return description to be used in drop-down box for selecting among PriorProviders **/ public String getDescription(); diff --git a/src/beast/app/draw/BEASTObjectInputEditor.java b/src/beast/app/draw/BEASTObjectInputEditor.java index d349f1da0..71760f370 100644 --- a/src/beast/app/draw/BEASTObjectInputEditor.java +++ b/src/beast/app/draw/BEASTObjectInputEditor.java @@ -16,7 +16,7 @@ import beast.app.beauti.BeautiSubTemplate; import beast.core.BEASTInterface; import beast.core.Input; -import beast.util.AddOnManager; +import beast.util.PackageManager; public class BEASTObjectInputEditor extends InputEditor.Base { private static final long serialVersionUID = 1L; @@ -472,7 +472,7 @@ protected void addComboBox(JComponent box, Input input, BEASTInterface beastO // } String[] getAvailablePlugins() { - List beastObjectNames = AddOnManager.find(m_input.getType(), "beast"); + List beastObjectNames = PackageManager.find(m_input.getType(), "beast"); return beastObjectNames.toArray(new String[0]); } // getAvailablePlugins diff --git a/src/beast/app/draw/BEASTObjectPanel.java b/src/beast/app/draw/BEASTObjectPanel.java index 9acf5c062..3a2d6b777 100644 --- a/src/beast/app/draw/BEASTObjectPanel.java +++ b/src/beast/app/draw/BEASTObjectPanel.java @@ -3,6 +3,7 @@ + import java.awt.Dimension; import java.awt.Point; import java.io.File; diff --git a/src/beast/app/draw/Document.java b/src/beast/app/draw/Document.java index b876bd5ae..4b1040310 100644 --- a/src/beast/app/draw/Document.java +++ b/src/beast/app/draw/Document.java @@ -50,7 +50,7 @@ import beast.core.Input; import beast.core.Runnable; import beast.core.util.Log; -import beast.util.AddOnManager; +import beast.util.PackageManager; import beast.util.XMLParser; import beast.util.XMLProducer; @@ -104,7 +104,7 @@ boolean sanitiseIDs() { public Document() { // load all parsers - List plugInNames = AddOnManager.find(beast.core.BEASTInterface.class, AddOnManager.IMPLEMENTATION_DIR); + List plugInNames = PackageManager.find(beast.core.BEASTInterface.class, PackageManager.IMPLEMENTATION_DIR); m_sPlugInNames = plugInNames.toArray(new String[0]); tabulist = new HashSet<>(); Properties properties = new Properties(); diff --git a/src/beast/app/draw/InputEditorFactory.java b/src/beast/app/draw/InputEditorFactory.java index 10ff44d42..46f99b785 100644 --- a/src/beast/app/draw/InputEditorFactory.java +++ b/src/beast/app/draw/InputEditorFactory.java @@ -22,7 +22,7 @@ import beast.core.Input; import beast.core.Input.Validate; import beast.core.util.Log; -import beast.util.AddOnManager; +import beast.util.PackageManager; @@ -51,7 +51,7 @@ public void init() { // registerInputEditors(knownEditors); String[] PACKAGE_DIRS = {"beast.app",}; for (String packageName : PACKAGE_DIRS) { - List inputEditors = AddOnManager.find("beast.app.draw.InputEditor", packageName); + List inputEditors = PackageManager.find("beast.app.draw.InputEditor", packageName); registerInputEditors(inputEditors.toArray(new String[0])); } } @@ -313,7 +313,7 @@ public List getAvailablePlugins(Input input, BEASTInterface parent, L } /* add all beastObject-classes of type assignable to the input */ if (doc.isExpertMode()) { - List classes = AddOnManager.find(input.getType(), "beast"); + List classes = PackageManager.find(input.getType(), "beast"); for (String className : classes) { try { Object o = Class.forName(className).newInstance(); diff --git a/src/beast/app/draw/ModelBuilder.java b/src/beast/app/draw/ModelBuilder.java index 625a3b479..4afa3bf35 100644 --- a/src/beast/app/draw/ModelBuilder.java +++ b/src/beast/app/draw/ModelBuilder.java @@ -80,7 +80,7 @@ import beast.app.util.Utils; import beast.core.BEASTInterface; import beast.evolution.alignment.Sequence; -import beast.util.AddOnManager; +import beast.util.PackageManager; import beast.util.Randomizer; import beast.util.XMLProducer; @@ -2153,7 +2153,7 @@ public JMenuBar makeMenuBar() { public static void main(String args[]) { Randomizer.setSeed(127); try { - AddOnManager.loadExternalJars(); + PackageManager.loadExternalJars(); } catch (Exception e) { e.printStackTrace(); } diff --git a/src/beast/app/tools/AppLauncher.java b/src/beast/app/tools/AppLauncher.java index b715844bd..113b8c596 100644 --- a/src/beast/app/tools/AppLauncher.java +++ b/src/beast/app/tools/AppLauncher.java @@ -41,7 +41,7 @@ import beast.app.util.Utils; import beast.core.util.Log; -import beast.util.AddOnManager; +import beast.util.PackageManager; /** @@ -248,7 +248,7 @@ private Box createButtonBox() { List getPackageApps() { List packageApps = new ArrayList<>(); - List dirs = AddOnManager.getBeastDirectories(); + List dirs = PackageManager.getBeastDirectories(); for (String jarDirName : dirs) { File versionFile = new File(jarDirName + "/version.xml"); if (versionFile.exists() && versionFile.isFile()) { @@ -257,19 +257,22 @@ List getPackageApps() { try { doc = factory.newDocumentBuilder().parse(versionFile); doc.normalize(); - // get addonapp info from version.xml - Element addon = doc.getDocumentElement(); - NodeList nodes = doc.getElementsByTagName("addonapp"); + // get package-app info from version.xml + Element packageElement = doc.getDocumentElement(); + NodeList nodes = doc.getElementsByTagName("packageapp"); + if (nodes.getLength() == 0) { + nodes = doc.getElementsByTagName("addonapp"); + } for (int j = 0; j < nodes.getLength(); j++) { - Element addOnAppElement = (Element) nodes.item(j); + Element pacakgeAppElement = (Element) nodes.item(j); PackageApp packageApp = new PackageApp(); - packageApp.packageName = addon.getAttribute("name"); + packageApp.packageName = packageElement.getAttribute("name"); packageApp.jarDir = jarDirName; - packageApp.className = addOnAppElement.getAttribute("class"); - packageApp.description = addOnAppElement.getAttribute("description"); - packageApp.argumentsString = addOnAppElement.getAttribute("args"); + packageApp.className = pacakgeAppElement.getAttribute("class"); + packageApp.description = pacakgeAppElement.getAttribute("description"); + packageApp.argumentsString = pacakgeAppElement.getAttribute("args"); - String iconLocation = addOnAppElement.getAttribute("icon"); + String iconLocation = pacakgeAppElement.getAttribute("icon"); packageApp.icon = Utils.getIcon(iconLocation); if (packageApp.icon == null || iconLocation.trim().isEmpty()) packageApp.icon = Utils.getIcon(DEFAULT_ICON); @@ -331,7 +334,7 @@ public void run() { public void runAppFromCMD(PackageApp packageApp, String[] additionalArgs) { try { - AddOnManager.loadExternalJars(); + PackageManager.loadExternalJars(); List cmd = new ArrayList<>(); if (System.getenv("JAVA_HOME") != null) { diff --git a/src/beast/app/util/Utils.java b/src/beast/app/util/Utils.java index 6a58d73ff..293e05e91 100644 --- a/src/beast/app/util/Utils.java +++ b/src/beast/app/util/Utils.java @@ -1,15 +1,13 @@ package beast.app.util; + import java.awt.Component; import java.awt.Font; import java.awt.Graphics; -import java.awt.GraphicsEnvironment; import java.awt.Image; import java.awt.Toolkit; import java.io.BufferedReader; import java.io.File; -import java.io.FileInputStream; -import java.io.FileOutputStream; import java.io.FilenameFilter; import java.io.IOException; import java.io.InputStream; @@ -17,12 +15,10 @@ import java.lang.reflect.Method; import java.net.URL; import java.util.HashSet; -import java.util.Properties; import java.util.Set; import javax.swing.ImageIcon; import javax.swing.JFileChooser; -import javax.swing.JOptionPane; import javax.swing.LookAndFeel; import javax.swing.UIManager; import javax.swing.UnsupportedLookAndFeelException; @@ -36,7 +32,6 @@ import beast.evolution.likelihood.BeagleTreeLikelihood; import beast.evolution.sitemodel.SiteModel; import beast.evolution.substitutionmodel.JukesCantor; -import beast.util.AddOnManager; import beast.util.TreeParser; /** diff --git a/src/beast/evolution/alignment/Alignment.java b/src/beast/evolution/alignment/Alignment.java index 614dd124f..e4862be41 100644 --- a/src/beast/evolution/alignment/Alignment.java +++ b/src/beast/evolution/alignment/Alignment.java @@ -31,7 +31,7 @@ import beast.core.util.Log; import beast.evolution.datatype.DataType; import beast.evolution.datatype.StandardData; -import beast.util.AddOnManager; +import beast.util.PackageManager; import java.util.*; @@ -64,7 +64,7 @@ protected Class mapType() { static public void findDataTypes() { // build up list of data types - List m_sDataTypes = AddOnManager.find(beast.evolution.datatype.DataType.class, IMPLEMENTATION_DIR); + List m_sDataTypes = PackageManager.find(beast.evolution.datatype.DataType.class, IMPLEMENTATION_DIR); for (String dataTypeName : m_sDataTypes) { try { DataType dataType = (DataType) Class.forName(dataTypeName).newInstance(); @@ -230,7 +230,7 @@ public void initAndValidate() { "Choose one of " + Arrays.toString(types.toArray(new String[0]))); } // seems to spend forever in there?? - List dataTypes = AddOnManager.find(beast.evolution.datatype.DataType.class, IMPLEMENTATION_DIR); + List dataTypes = PackageManager.find(beast.evolution.datatype.DataType.class, IMPLEMENTATION_DIR); for (String dataTypeName : dataTypes) { DataType dataType; try { diff --git a/src/beast/util/JSONParser.java b/src/beast/util/JSONParser.java index 3049918f2..a43db6ab0 100644 --- a/src/beast/util/JSONParser.java +++ b/src/beast/util/JSONParser.java @@ -854,7 +854,7 @@ BEASTInterface createObject(JSONObject node, String className) throws JSONParser // } } } catch (ClassNotFoundException e1) { - // should never happen since clazzName is in the list of classes collected by the AddOnManager + // should never happen since clazzName is in the list of classes collected by the PackageManager e1.printStackTrace(); throw new RuntimeException(e1); } diff --git a/src/beast/util/Package.java b/src/beast/util/Package.java index f2911b640..4688b22f6 100644 --- a/src/beast/util/Package.java +++ b/src/beast/util/Package.java @@ -6,7 +6,7 @@ import java.util.*; /** - * BEAUti Package managed by AddOnManager. + * BEAUti Package managed by PackageManager. * * Add a new rule in issue 754: * Package manager should make project links compulsory. @@ -197,7 +197,7 @@ public String getDependenciesString() { String depString = ""; for (PackageDependency packageDependency : availableVersionDeps.lastEntry().getValue()) { String s = packageDependency.dependencyName; - if (!s.equalsIgnoreCase(AddOnManager.BEAST_PACKAGE_NAME)) { + if (!s.equalsIgnoreCase(PackageManager.BEAST_PACKAGE_NAME)) { depString += s + ", "; } } diff --git a/src/beast/util/PackageDependency.java b/src/beast/util/PackageDependency.java index 9797843ec..d109cec78 100644 --- a/src/beast/util/PackageDependency.java +++ b/src/beast/util/PackageDependency.java @@ -45,7 +45,7 @@ public PackageDependency(String dependencyName, PackageVersion minimumVersion, PackageVersion maximumVersion) { if (dependencyName.equals("beast2")) { - dependencyName = AddOnManager.BEAST_PACKAGE_NAME; + dependencyName = PackageManager.BEAST_PACKAGE_NAME; } this.dependencyName = dependencyName; diff --git a/src/beast/util/AddOnManager.java b/src/beast/util/PackageManager.java similarity index 95% rename from src/beast/util/AddOnManager.java rename to src/beast/util/PackageManager.java index 85f26f4fb..5fab01e88 100644 --- a/src/beast/util/AddOnManager.java +++ b/src/beast/util/PackageManager.java @@ -1,5 +1,5 @@ /* - * File AddOnManager.java + * File PackageManager.java * * Copyright (C) 2010 Remco Bouckaert remco@cs.auckland.ac.nz * @@ -73,7 +73,7 @@ */ // TODO: on windows allow installation on drive D: and pick up add-ons in drive C: //@Description("Manage all BEAUti packages and list their dependencies") -public class AddOnManager { +public class PackageManager { public static final BEASTVersion beastVersion = BEASTVersion.INSTANCE; public enum UpdateStatus {AUTO_CHECK_AND_ASK, AUTO_UPDATE, DO_NOT_CHECK}; @@ -212,9 +212,9 @@ public static void addInstalledPackages(Map packageMap) { Document doc = factory.newDocumentBuilder().parse(versionXML); doc.normalize(); // get name and version of package - Element addon = doc.getDocumentElement(); - String packageName = addon.getAttribute("name"); - String packageVersionString = addon.getAttribute("version"); + Element packageElement = doc.getDocumentElement(); + String packageName = packageElement.getAttribute("name"); + String packageVersionString = packageElement.getAttribute("version"); Package pkg; if (packageMap.containsKey(packageName)) { @@ -224,14 +224,14 @@ public static void addInstalledPackages(Map packageMap) { packageMap.put(packageName, pkg); } - if (addon.hasAttribute("projectURL")) - pkg.setProjectURL(new URL(addon.getAttribute("projectURL"))); + if (packageElement.hasAttribute("projectURL")) + pkg.setProjectURL(new URL(packageElement.getAttribute("projectURL"))); PackageVersion installedVersion = new PackageVersion(packageVersionString); - if (addon.hasAttribute("projectURL") && + if (packageElement.hasAttribute("projectURL") && !(pkg.getLatestVersion() != null && installedVersion.compareTo(pkg.getLatestVersion())<0)) - pkg.setProjectURL(new URL(addon.getAttribute("projectURL"))); + pkg.setProjectURL(new URL(packageElement.getAttribute("projectURL"))); Set installedVersionDependencies = new TreeSet(new Comparator() { @@ -604,7 +604,7 @@ public static String uninstallPackage(Package pkg, PackageVersion pkgVersion, bo * http://docs.oracle.com/javase/7/docs/api/java/net/URLClassLoader.html#close%28%29 * * This allows smooth upgrading of BEAST versions using the package manager. Without - * this, there is no way to upgrade BEAST since the AddOnManager is part of the + * this, there is no way to upgrade BEAST since the PackageManager is part of the * BEAST.jar file that is loaded and needs to be replaced. * * Side effect is that after installing a package, opening a new BEAUti instance @@ -614,7 +614,7 @@ public static String uninstallPackage(Package pkg, PackageVersion pkgVersion, bo private static void closeClassLoader() { try { if (Utils6.isWindows()) { - URLClassLoader sysLoader = (URLClassLoader) AddOnManager.class.getClassLoader(); + URLClassLoader sysLoader = (URLClassLoader) PackageManager.class.getClassLoader(); sysLoader.close(); } } catch (IOException e) { @@ -854,14 +854,8 @@ public static List getBeastDirectories() { List dirs = new ArrayList(); // check if there is the BEAST environment variable is set - if (System.getProperty("BEAST_ADDON_PATH") != null) { - String BEAST = System.getProperty("BEAST_ADDON_PATH"); - for (String dirName : BEAST.split(":")) { - dirs.add(dirName); - } - } - if (System.getenv("BEAST_ADDON_PATH") != null) { - String BEAST = System.getenv("BEAST_ADDON_PATH"); + if (PackageManager.getBeastPacakgePathProperty() != null) { + String BEAST = PackageManager.getBeastPacakgePathProperty(); for (String dirName : BEAST.split(":")) { dirs.add(dirName); } @@ -945,8 +939,8 @@ private static List getLatestBeastArchiveDirectories(List visite // find name of package DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); Document doc = factory.newDocumentBuilder().parse(versionFile); - Element addon = doc.getDocumentElement(); - alreadyLoaded.add(addon.getAttribute("name")); + Element packageElement = doc.getDocumentElement(); + alreadyLoaded.add(packageElement.getAttribute("name")); } catch (Exception e) { // too bad, won't print out any info } @@ -962,8 +956,8 @@ private static List getLatestBeastArchiveDirectories(List visite // find name of package DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); Document doc = factory.newDocumentBuilder().parse(versionFile); - Element addon = doc.getDocumentElement(); - alreadyLoaded.add(addon.getAttribute("name")); + Element packageElement = doc.getDocumentElement(); + alreadyLoaded.add(packageElement.getAttribute("name")); } catch (Exception e) { // too bad, won't print out any info } @@ -1075,7 +1069,7 @@ public static void loadExternalJars(String packagesString) throws IOException { Package pkg = new Package(pkgname); PackageVersion version = new PackageVersion(pkgversion); useArchive = true; - String dirName = getPackageDir(pkg, version, false, System.getProperty("BEAST_ADDON_PATH")); + String dirName = getPackageDir(pkg, version, false, PackageManager.getBeastPacakgePathProperty()); if (new File(dirName).exists()) { loadPackage(dirName); } else { @@ -1085,7 +1079,7 @@ public static void loadExternalJars(String packagesString) throws IOException { unavailablePacakges += s +", "; } else { useArchive = false; - dirName = getPackageDir(pkg, version, false, System.getProperty("BEAST_ADDON_PATH")); + dirName = getPackageDir(pkg, version, false, PackageManager.getBeastPacakgePathProperty()); if (new File(dirName).exists()) { loadPackage(dirName); } else { @@ -1118,8 +1112,8 @@ private static void loadPackage(String jarDirName) { // print name and version of package DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); Document doc = factory.newDocumentBuilder().parse(versionFile); - Element addon = doc.getDocumentElement(); - packageNameAndVersion = addon.getAttribute("name") + " v" + addon.getAttribute("version"); + Element packageElement = doc.getDocumentElement(); + packageNameAndVersion = packageElement.getAttribute("name") + " v" + packageElement.getAttribute("version"); Log.warning.println("Loading package " + packageNameAndVersion); Utils6.logToSplashScreen("Loading package " + packageNameAndVersion); } catch (Exception e) { @@ -1333,7 +1327,7 @@ private static void message(String string) { */ public static void addURL(URL u) throws IOException { // ClassloaderUtil clu = new ClassloaderUtil(); - AddOnManager clu = new AddOnManager(); + PackageManager clu = new PackageManager(); // URLClassLoader sysLoader = (URLClassLoader) // ClassLoader.getSystemClassLoader(); URLClassLoader sysLoader = (URLClassLoader) clu.getClass().getClassLoader(); @@ -1429,18 +1423,23 @@ private static void loadAllClasses() { } private static void addDirContent(File dir, int len) { + try { // No point in checking directories that cannot be read. // Need check here since these potentially can cause exceptions - if (dir.canRead()) { - for (File file : dir.listFiles()) { - if (file.isDirectory()) { - addDirContent(file, len); - } else { - if (file.getName().endsWith(".class")) { - all_classes.add(file.getAbsolutePath().substring(len)); - } - } - } + if (dir.canRead()) { + for (File file : dir.listFiles()) { + if (file.isDirectory()) { + addDirContent(file, len); + } else { + if (file.getName().endsWith(".class")) { + all_classes.add(file.getAbsolutePath().substring(len)); + } + } + } + } + } catch (Exception e) { + // ignore + // windows appears to throw exceptions on unaccessible directories } } @@ -1757,12 +1756,12 @@ public static void prettyPrintPackageInfo(PrintStream ps, Map p private static void printUsageAndExit(Arguments arguments) { - arguments.printUsage("addonmanager", ""); + arguments.printUsage("packagemanager", ""); Log.info.println("\nExamples:"); - Log.info.println("addonmanager -list"); - Log.info.println("addonmanager -add SNAPP"); - Log.info.println("addonmanager -useAppDir -add SNAPP"); - Log.info.println("addonmanager -del SNAPP"); + Log.info.println("packagemanager -list"); + Log.info.println("packagemanager -add SNAPP"); + Log.info.println("packagemanager -useAppDir -add SNAPP"); + Log.info.println("packagemanager -del SNAPP"); System.exit(0); } @@ -1806,8 +1805,8 @@ public static void main(String[] args) { boolean useAppDir = arguments.hasOption("useAppDir"); String customDir = arguments.getStringOption("dir"); if (customDir != null) { - String path = System.getProperty("BEAST_ADDON_PATH"); - System.setProperty("BEAST_ADDON_PATH", (path != null ? path + ":" : "") +customDir); + String path = PackageManager.getBeastPacakgePathProperty(); + System.setProperty("BEAST_PACKAGE_PATH", (path != null ? path + ":" : "") +customDir); } List urlList = getRepositoryURLs(); @@ -1824,8 +1823,8 @@ public int compare(String s1, String s2) { } }); try { - AddOnManager.addInstalledPackages(packageMap); - AddOnManager.addAvailablePackages(packageMap); + PackageManager.addInstalledPackages(packageMap); + PackageManager.addAvailablePackages(packageMap); } catch (PackageListRetrievalException e) { Log.warning.println(e.getMessage()); if (e.getCause() instanceof IOException) @@ -1851,7 +1850,7 @@ public int compare(String s1, String s2) { String versionString = arguments.getStringOption("version"); PackageVersion version = new PackageVersion(versionString); packagesToInstall.put(aPackage, version); - AddOnManager.useArchive = true; + PackageManager.useArchive = true; } else { packagesToInstall.put(aPackage, aPackage.getLatestVersion()); } @@ -1883,7 +1882,7 @@ public int compare(String s1, String s2) { if (aPackage.packageName.equals(name)) { processed = true; if (arguments.hasOption("version")) { - AddOnManager.useArchive = true; + PackageManager.useArchive = true; String versionString = arguments.getStringOption("version"); PackageVersion version = new PackageVersion(versionString); String dir = uninstallPackage(aPackage, version, useAppDir, customDir); @@ -1947,8 +1946,8 @@ private static void initPackageMap(String jarDirName) { // print name and version of package DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); Document doc = factory.newDocumentBuilder().parse(versionFile); - Element addon = doc.getDocumentElement(); - packageNameAndVersion = addon.getAttribute("name") + " v" + addon.getAttribute("version"); + Element packageElement = doc.getDocumentElement(); + packageNameAndVersion = packageElement.getAttribute("name") + " v" + packageElement.getAttribute("version"); Log.warning.println("Loading package " + packageNameAndVersion); Utils6.logToSplashScreen("Loading package " + packageNameAndVersion); } catch (Exception e) { @@ -2029,13 +2028,13 @@ public static void updatePackages(UpdateStatus updateStatus, boolean useGUI) { new Comparator() { @Override public int compare(String s1, String s2) { - if (s1.equals(AddOnManager.BEAST_PACKAGE_NAME)) { - if (s2.equals(AddOnManager.BEAST_PACKAGE_NAME)) { + if (s1.equals(PackageManager.BEAST_PACKAGE_NAME)) { + if (s2.equals(PackageManager.BEAST_PACKAGE_NAME)) { return 0; } return -1; } - if (s2.equals(AddOnManager.BEAST_PACKAGE_NAME)) { + if (s2.equals(PackageManager.BEAST_PACKAGE_NAME)) { return 1; } return s1.compareToIgnoreCase(s2); @@ -2145,4 +2144,16 @@ public int compare(String s1, String s2) { } } + public static String getBeastPacakgePathProperty() { + if (System.getProperty("BEAST_PACKAGE_PATH") != null) { + return System.getProperty("BEAST_PACKAGE_PATH"); + } + if (System.getenv("BEAST_PACKAGE_PATH") != null) { + return System.getenv("BEAST_PACKAGE_PATH"); + } + if (System.getenv("BEAST_ADDON_PATH") != null) { + return System.getenv("BEAST_ADDON_PATH"); + } + return System.getenv("BEAST_ADDON_PATH"); + } } diff --git a/src/beast/util/XMLParser.java b/src/beast/util/XMLParser.java index 5881e73fd..b17d6cd35 100644 --- a/src/beast/util/XMLParser.java +++ b/src/beast/util/XMLParser.java @@ -511,7 +511,7 @@ public void parse() throws XMLParserException { if (i > 0) { String pkgname = s.substring(0, i); String pkgversion = s.substring(i+1); - if (!AddOnManager.isInstalled(pkgname, pkgversion)) { + if (!PackageManager.isInstalled(pkgname, pkgversion)) { unavailablePacakges += s +", "; } } @@ -772,7 +772,7 @@ BEASTInterface createObject(final Node node, final String classname) throws XMLP throw new XMLParserException(node, "Expected object to be instance of BEASTObject", 108); } } catch (ClassNotFoundException e1) { - // should never happen since clazzName is in the list of classes collected by the AddOnManager + // should never happen since clazzName is in the list of classes collected by the PackageManager e1.printStackTrace(); throw new RuntimeException(e1); } diff --git a/src/beast/util/XMLParserUtils.java b/src/beast/util/XMLParserUtils.java index f2242341b..d281da0fa 100644 --- a/src/beast/util/XMLParserUtils.java +++ b/src/beast/util/XMLParserUtils.java @@ -39,7 +39,7 @@ */ public class XMLParserUtils { - final static public List beastObjectNames = AddOnManager.find(beast.core.BEASTInterface.class, AddOnManager.IMPLEMENTATION_DIR); + final static public List beastObjectNames = PackageManager.find(beast.core.BEASTInterface.class, PackageManager.IMPLEMENTATION_DIR); /** diff --git a/src/beast/util/XMLProducer.java b/src/beast/util/XMLProducer.java index e6ce8dcd7..9daeed38d 100644 --- a/src/beast/util/XMLProducer.java +++ b/src/beast/util/XMLProducer.java @@ -111,7 +111,7 @@ public Set getPackagesAndVersions(BEASTInterface o) { * along the way. */ private void getPackagesAndVersions(BEASTInterface o, Set packagesAndVersions) { - Map classToPackageMap = AddOnManager.getClassToPackageMap(); + Map classToPackageMap = PackageManager.getClassToPackageMap(); String packageAndVersion = classToPackageMap.get(o.getClass().getName()); if (packageAndVersion != null) { packagesAndVersions.add(packageAndVersion); diff --git a/src/test/beast/integration/DocumentationTest.java b/src/test/beast/integration/DocumentationTest.java index 46b6dc409..14a2fc313 100644 --- a/src/test/beast/integration/DocumentationTest.java +++ b/src/test/beast/integration/DocumentationTest.java @@ -9,7 +9,7 @@ import beast.core.BEASTObject; import beast.core.Description; import beast.core.Input; -import beast.util.AddOnManager; +import beast.util.PackageManager; import junit.framework.TestCase; @@ -27,7 +27,7 @@ public class DocumentationTest extends TestCase { */ @Test public void testDescriptions() { - final List pluginNames = AddOnManager.find(beast.core.BEASTObject.class, AddOnManager.IMPLEMENTATION_DIR); + final List pluginNames = PackageManager.find(beast.core.BEASTObject.class, PackageManager.IMPLEMENTATION_DIR); final List undocumentedPlugins = new ArrayList(); for (final String beastObjectName : pluginNames) { try { @@ -58,7 +58,7 @@ public void testDescriptions() { */ @Test public void testInputTipText() { - final List pluginNames = AddOnManager.find(beast.core.BEASTObject.class, AddOnManager.IMPLEMENTATION_DIR); + final List pluginNames = PackageManager.find(beast.core.BEASTObject.class, PackageManager.IMPLEMENTATION_DIR); final List undocumentedInputs = new ArrayList(); for (final String beastObjectName : pluginNames) { try { diff --git a/src/test/beast/integration/InputTypeTest.java b/src/test/beast/integration/InputTypeTest.java index 156c63a1b..0ac257891 100644 --- a/src/test/beast/integration/InputTypeTest.java +++ b/src/test/beast/integration/InputTypeTest.java @@ -14,7 +14,7 @@ import beast.core.BEASTObject; import beast.core.Input; import beast.core.Param; -import beast.util.AddOnManager; +import beast.util.PackageManager; import junit.framework.TestCase; public class InputTypeTest extends TestCase { @@ -30,8 +30,8 @@ public class InputTypeTest extends TestCase { */ @Test public void testInputTypeCanBeSet() throws Exception { - List beastObjectNames = AddOnManager.find(beast.core.BEASTObject.class, - AddOnManager.IMPLEMENTATION_DIR); + List beastObjectNames = PackageManager.find(beast.core.BEASTObject.class, + PackageManager.IMPLEMENTATION_DIR); List failingInputs = new ArrayList(); for (String beastObjectName : beastObjectNames) { try { @@ -62,11 +62,11 @@ public void testInputTypeCanBeSet() throws Exception { @Test public void testAnnotatedInputHasGetters() throws Exception { - testAnnotatedInputHasGetters(AddOnManager.IMPLEMENTATION_DIR); + testAnnotatedInputHasGetters(PackageManager.IMPLEMENTATION_DIR); } public void testAnnotatedInputHasGetters(String [] packages) throws Exception { - List beastObjectNames = AddOnManager.find(Object.class, packages); + List beastObjectNames = PackageManager.find(Object.class, packages); System.err.println("Testing " + beastObjectNames.size() + " classes"); List failingInputs = new ArrayList(); for (String beastObject : beastObjectNames) { diff --git a/src/test/beast/integration/XMLElementNameTest.java b/src/test/beast/integration/XMLElementNameTest.java index f201a708d..2b5efb438 100644 --- a/src/test/beast/integration/XMLElementNameTest.java +++ b/src/test/beast/integration/XMLElementNameTest.java @@ -10,7 +10,7 @@ import beast.core.BEASTObject; import beast.core.Input; -import beast.util.AddOnManager; +import beast.util.PackageManager; import beast.util.XMLParser; import junit.framework.TestCase; @@ -22,7 +22,7 @@ public class XMLElementNameTest extends TestCase { */ @Test public void test_NameUniqueness() { - List pluginNames = AddOnManager.find(beast.core.BEASTObject.class, AddOnManager.IMPLEMENTATION_DIR); + List pluginNames = PackageManager.find(beast.core.BEASTObject.class, PackageManager.IMPLEMENTATION_DIR); List improperInputs = new ArrayList(); for (String beastObjectName : pluginNames) { try { @@ -66,7 +66,7 @@ public void test_ReservedElementNames() { element2ClassMap.put("parameter", "beast.core.parameter.Parameter"); // check each beastObject - List pluginNames = AddOnManager.find(beast.core.BEASTObject.class, AddOnManager.IMPLEMENTATION_DIR); + List pluginNames = PackageManager.find(beast.core.BEASTObject.class, PackageManager.IMPLEMENTATION_DIR); List improperInputs = new ArrayList(); for (String beastObjectName : pluginNames) { try { diff --git a/version.xml b/version.xml index 3320aa16a..ae9af1a50 100644 --- a/version.xml +++ b/version.xml @@ -1 +1 @@ - +