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rename AddOnManager to PackageManager #40
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@rbouckaert
rbouckaert committed Mar 13, 2018
1 parent ed94bb0 commit ba18dcf
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Showing 33 changed files with 174 additions and 164 deletions.
5 changes: 1 addition & 4 deletions build.xml
View file
Expand Up @@ -93,7 +93,6 @@
<fileset dir="${build}/beast/core/util/" includes="Log*.class" />
<fileset dir="${build}/beast/app/beastapp/" includes="BeastLauncher*.class" />
<fileset dir="${build}/beast/app/util/" includes="Arguments*.class"/>
<fileset dir="${build}/beast/util/" includes="AddOnManager*.class"/>
<fileset dir="${build}/beast/util/" includes="Package*.class"/>
</delete>
<delete file="${build}/beast/app/util/Version.class" />
Expand All @@ -114,7 +113,6 @@
<include name="beast/util/Package*.java" />
<include name="beast/app/util/Arguments.java" />
<include name="beast/core/util/Log.java" />
<include name="beast/util/AddOnManager.java" />
</javac>
<copy todir="${build}">
<fileset dir="${src}" includes="**/*.properties" />
Expand Down Expand Up @@ -157,7 +155,6 @@
<include name="beast/**/Version.class" />
<include name="beast/app/util/Arguments*.class" />
<include name="beast/util/Package*.class" />
<include name="beast/util/AddOnManager*.class" />
<include name="beast/app/draw/icons/beauti.png"/>
<include name="beast/core/util/Log*.class" />
</fileset>
Expand All @@ -179,7 +176,7 @@
<copy file="${dist}/beast.jar" todir="${release_dir}/package/lib/"/>
<copy file="../beast2/version.xml" todir="${release_dir}/package/"/>

<jar jarfile="${release_dir}/package/BEAST.addon.v${version}.zip">
<jar jarfile="${release_dir}/package/BEAST.package.v${version}.zip">
<fileset dir="${release_dir}/package">
<include name="version.xml" />
<include name="lib/beast.jar" />
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2 changes: 1 addition & 1 deletion release/Linux/bin/addonmanager → release/Linux/bin/packagemanager
View file
Expand Up @@ -29,5 +29,5 @@ if [ -z "$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 $*

2 changes: 1 addition & 1 deletion release/Linux/jrebin/addonmanager → release/Linux/jrebin/packagemanager
View file
Expand Up @@ -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 $*

6 changes: 3 additions & 3 deletions src/beast/app/BeastMCMC.java
View file
Expand Up @@ -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;
Expand Down Expand Up @@ -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();
}


Expand Down
6 changes: 3 additions & 3 deletions src/beast/app/DocMaker.java
View file
Expand Up @@ -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;



Expand Down Expand Up @@ -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<>();
Expand Down Expand Up @@ -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!!!");
Expand Down
4 changes: 2 additions & 2 deletions src/beast/app/ModelBuilder.java
View file
Expand Up @@ -35,7 +35,7 @@
import javax.swing.JPanel;
import javax.swing.UIManager;

import beast.util.AddOnManager;
import beast.util.PackageManager;
import beast.util.Randomizer;


Expand All @@ -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
}
Expand Down
33 changes: 16 additions & 17 deletions src/beast/app/beastapp/BeastLauncher.java
View file
Expand Up @@ -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;
Expand All @@ -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;

Expand Down Expand Up @@ -144,7 +143,7 @@ private static void createBeastPackage(File jarDir0) {
File target = new File(dir + pathDelimiter + "beast.jar");
copyFileUsingStream(beastJar, target);

String version = "<addon name='BEAST' version='" + BEASTVersion.INSTANCE.getVersion() + "'>\n" + "</addon>";
String version = "<package name='BEAST' version='" + BEASTVersion.INSTANCE.getVersion() + "'>\n" + "</package>";
FileWriter outfile = new FileWriter(userDir + pathDelimiter + "BEAST" + pathDelimiter + "version.xml");
outfile.write(version);
outfile.close();
Expand Down Expand Up @@ -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) {
Expand Down Expand Up @@ -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();
Expand All @@ -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<String, Package> packages = new HashMap<String, Package>();
AddOnManager.addInstalledPackages(packages);
PackageManager.addInstalledPackages(packages);

String unavailablePackages = "";
String [] packageAndVersions = packagesString.split(":");
Expand All @@ -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 {
Expand All @@ -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 {
Expand All @@ -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<String> classes = new HashSet<String>();
for (String jarDirName : AddOnManager.getBeastDirectories()) {
for (String jarDirName : PackageManager.getBeastDirectories()) {
try {
File versionFile = new File(jarDirName + "/version.xml");
String packageNameAndVersion = null;
Expand All @@ -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 " +
Expand Down
22 changes: 11 additions & 11 deletions src/beast/app/beauti/Beauti.java
View file
Expand Up @@ -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;


Expand Down Expand Up @@ -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();
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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);
Expand Down Expand Up @@ -1001,7 +1001,7 @@ public void actionPerformed(ActionEvent e) {

private List<AbstractAction> getTemplateActions() {
List<AbstractAction> actions = new ArrayList<>();
List<String> beastDirectories = AddOnManager.getBeastDirectories();
List<String> beastDirectories = PackageManager.getBeastDirectories();
for (String dirName : beastDirectories) {
File dir = new File(dirName + "/templates");
getTemplateActionForDir(dir, actions);
Expand Down Expand Up @@ -1042,7 +1042,7 @@ private void getTemplateActionForDir(File dir, List<AbstractAction> actions) {

private List<AbstractAction> getWorkDirActions() {
List<AbstractAction> actions = new ArrayList<>();
List<String> beastDirectories = AddOnManager.getBeastDirectories();
List<String> beastDirectories = PackageManager.getBeastDirectories();
Set<String> doneDirs = new HashSet<>();
for (String dir : beastDirectories) {
if (!doneDirs.contains(dir)) {
Expand Down Expand Up @@ -1220,7 +1220,7 @@ public void close() throws IOException {
}
}

AddOnManager.loadExternalJars();
PackageManager.loadExternalJars();
//if (!Utils.isMac()) {
Utils.loadUIManager();
//}
Expand Down Expand Up @@ -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();
}
Expand Down
4 changes: 2 additions & 2 deletions src/beast/app/beauti/BeautiAlignmentProvider.java
View file
Expand Up @@ -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;

Expand All @@ -60,7 +60,7 @@ private void initImporters() {
importers.add(new FastaImporter());

// build up list of data types
List<String> importerClasses = AddOnManager.find(AlignmentImporter.class, IMPLEMENTATION_DIR);
List<String> importerClasses = PackageManager.find(AlignmentImporter.class, IMPLEMENTATION_DIR);
for (String _class: importerClasses) {
try {
if (!_class.startsWith(this.getClass().getName())) {
Expand Down
4 changes: 2 additions & 2 deletions src/beast/app/beauti/BeautiDoc.java
View file
Expand Up @@ -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<String> dirs = new HashSet<>();// AddOnManager.getBeastDirectories();
Set<String> dirs = new HashSet<>();
String pathSep = System.getProperty("path.separator");
String classpath = System.getProperty("java.class.path");
String fileSep = System.getProperty("file.separator");
Expand Down Expand Up @@ -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<String> loadedTemplates = new HashSet<>();
for (String dirName : dirs) {
Log.info.println("Investigating " + dirName);
Expand Down

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