import java.lang.reflect.Method;
import java.net.MalformedURLException;
import java.net.Proxy;
+import java.net.SocketAddress;
+import java.net.InetSocketAddress;
+import java.net.URI;
+import java.net.URISyntaxException;
import java.net.URL;
import java.net.URLClassLoader;
import java.net.URLConnection;
+import java.net.URLDecoder;
import java.net.URLEncoder;
import java.nio.channels.FileChannel;
import java.nio.channels.FileLock;
import java.util.regex.Pattern;
import java.util.zip.GZIPInputStream;
+import jalview.bin.HiDPISetting;
import jalview.bin.MemorySetting;
-import com.install4j.api.launcher.Variables;
+import jalview.util.LaunchUtils;
import com.threerings.getdown.util.*;
// avoid ambiguity with java.util.Base64 which we can't use as it's 1.8+
{
return _initialisedConfig;
}
+
+ try {
+ Application.i4jVersion = com.install4j.api.launcher.Variables.getCompilerVariable("sys.install4jVersion");
+ } catch (IOException e)
+ {
+ System.err.println("install4j version not available");
+ } catch (NoClassDefFoundError e)
+ {
+ log.warning("Starting without install4j classes");
+ } catch (Throwable t)
+ {
+ System.err.println("install4j not available");
+ t.printStackTrace();
+ }
+
Config config = null;
File cfgfile = _config;
Config.ParseOpts opts = Config.createOpts(checkPlatform);
}
// see if a percentage of physical memory, or max heap size options exist
- String jvmmempc = config.getString("jvmmempc", null);
- String jvmmemmax = config.getString("jvmmemmax", null);
+ jvmmempc = config.getString("jvmmempc", null);
+ jvmmemmax = config.getString("jvmmemmax", null);
// app_id prefixed setting overrides
if (appPrefix.length() > 0) {
jvmmempc = config.getString(appPrefix + "jvmmempc", jvmmempc);
jvmmemmax = config.getString(appPrefix + "jvmmemmax", jvmmemmax);
}
- long maxMemLong = -1;
- maxMemLong = MemorySetting.getMemorySetting(jvmmemmax, jvmmempc);
- if (maxMemLong > 0)
- {
- String[] maxMemHeapArg = new String[]{"-Xmx"+Long.toString(maxMemLong)};
- // remove other max heap size arg
- ARG: for (int i = 0; i < _jvmargs.size(); i++) {
- if (_jvmargs.get(i) instanceof java.lang.String && _jvmargs.get(i).startsWith("-Xmx")) {
- _jvmargs.remove(i);
- break ARG;
- }
- }
- addAll(maxMemHeapArg, _jvmargs);
- }
// get the set of optimum JVM arguments
_optimumJvmArgs = config.getMultiValue("optimum_jvmarg");
}
// pass along our proxy settings
- String proxyHost;
- if ((proxyHost = System.getProperty("http.proxyHost")) != null) {
+ String proxyHost = System.getProperty("http.proxyHost");
+ String proxyPort = StringUtil.isBlank(System.getProperty("http.proxyPort")) ? "80" : System.getProperty("http.proxyPort");
+ if (StringUtil.isBlank(proxyHost) && ! proxy.equals(Proxy.NO_PROXY)) {
+ try {
+ SocketAddress a = proxy.address();
+ if (a != null && a instanceof InetSocketAddress) {
+ InetSocketAddress ia = (InetSocketAddress)a;
+ proxyHost = ia.getHostString();
+ proxyPort = String.valueOf(ia.getPort());
+ }
+ } catch (Exception e) {
+ log.error("Problem obtaining proxy settings from Proxy object");
+ e.printStackTrace();
+ }
+ }
+ if (proxyHost != null) {
+ log.info("Using proxy settings "+proxyHost+":"+proxyPort);
args.add("-Dhttp.proxyHost=" + proxyHost);
- args.add("-Dhttp.proxyPort=" + System.getProperty("http.proxyPort"));
+ args.add("-Dhttp.proxyPort=" + proxyPort);
args.add("-Dhttps.proxyHost=" + proxyHost);
- args.add("-Dhttps.proxyPort=" + System.getProperty("http.proxyPort"));
- }
+ args.add("-Dhttps.proxyPort=" + proxyPort);
+ } else {
+ log.info("Not setting proxy");
+ }
+
+ // add the getdownappbase property. getdownappdir is added by getdown.txt
+ args.add("-Dgetdownappbase=" + getAppbase().toString());
// add the marker indicating the app is running in getdown
args.add("-D" + Properties.GETDOWN + "=true");
- args.add("-Dsys.install4jVersion=" + Variables.getCompilerVariable("sys.install4jVersion"));
+ args.add("-Dsys.install4jVersion=" + Application.i4jVersion);
args.add("-Dinstaller_template_version=" + System.getProperty("installer_template_version"));
args.add("-Dlauncher_version=" + Build.version());
+ // set HiDPI property if wanted
+ String scalePropertyArg = HiDPISetting.getScalePropertyArg();
+ if (scalePropertyArg != null)
+ {
+ args.add(scalePropertyArg);
+ }
+
// set the native library path if we have native resources
// @TODO optional getdown.txt parameter to set addCurrentLibraryPath to true or false?
ClassPath javaLibPath = PathBuilder.buildLibsPath(this, true);
}
}
+ // test for jalview/s URL. Insert startupNotification URI into start of _appargs
+ if (! StringUtil.isBlank(_jalviewUri)) {
+ _appargs.add(0, _jalviewUri);
+ }
+ if (_appargs.size() > 0) {
+ String uri = _appargs.get(0);
+ try {
+ log.info("TRYING TO PARSE URL '"+uri+"'");
+ URI jalviewUri = new URI(uri);
+ if (jalviewUri != null) {
+ String scheme = jalviewUri.getScheme();
+ if (scheme != null && (scheme.equals("jalview") || scheme.equals("jalviews"))) {
+ boolean https = jalviewUri.getScheme().equals("jalviews");
+ String host = jalviewUri.getHost();
+ int port = jalviewUri.getPort();
+ String file = jalviewUri.getPath();
+ String ref = jalviewUri.getFragment();
+ String query = jalviewUri.getQuery();
+
+ _appargs.clear();
+ _appargs.add("-open");
+ if (host != null && host.length() > 0) {
+ URL newUrl = new URL(
+ (https?"https":"http")
+ + "://"
+ + host
+ + (port > -1? String.valueOf(port) : "")
+ + jalviewUri.getRawPath()
+ + (query != null && query.length() > 0 ? "?" + jalviewUri.getRawQuery() : "")
+ );
+ _appargs.add(newUrl.toString());
+ } else {
+ _appargs.add(file);
+ }
+
+ if (ref != null && ref.length() > 0) {
+ String[] refArgs = ref.split("&");
+ for (String refArg : refArgs) {
+ if (refArg.startsWith("jvmmempc=")) {
+ jvmmempc = refArg.substring(9);
+ continue;
+ }
+ if (refArg.startsWith("jvmmemmax=")) {
+ jvmmemmax = refArg.substring(10);
+ continue;
+ }
+ _appargs.add(URLDecoder.decode(refArg, "UTF-8"));
+ }
+ }
+
+ }
+ }
+ } catch (URISyntaxException e) {
+ log.error("Malformed jalview URI", uri);
+ }
+ }
+
+ for (String argString: _appargs) {
+ if (argString.startsWith("-jvmmempc=")) {
+ jvmmempc = argString.substring(10);
+ continue;
+ }
+ if (argString.startsWith("-jvmmemmax=")) {
+ jvmmemmax = argString.substring(11);
+ continue;
+ }
+ }
+
+ // use saved preferences if no cmdline args
+ LaunchUtils.loadChannelProps(getAppDir());
+ if (LaunchUtils.getBooleanUserPreference(MemorySetting.CUSTOMISED_SETTINGS)) {
+ if (jvmmempc == null) {
+ jvmmempc = LaunchUtils.getUserPreference(MemorySetting.MEMORY_JVMMEMPC);
+ }
+ if (jvmmemmax == null) {
+ jvmmemmax = LaunchUtils.getUserPreference(MemorySetting.MEMORY_JVMMEMMAX);
+ }
+ }
+
+ // add the memory setting from jvmmempc and jvmmemmax
+ long maxMemLong = -1;
+ maxMemLong = MemorySetting.getMemorySetting(jvmmemmax, jvmmempc);
+ if (maxMemLong > 0)
+ {
+ String[] maxMemHeapArg = new String[]{"-Xmx"+Long.toString(maxMemLong)};
+ // remove other max heap size arg
+ ARG: for (int i = 0; i < _jvmargs.size(); i++) {
+ if (_jvmargs.get(i) instanceof java.lang.String && _jvmargs.get(i).startsWith("-Xmx")) {
+ _jvmargs.remove(i);
+ break ARG;
+ }
+ }
+ addAll(maxMemHeapArg, _jvmargs);
+ }
+
// add the JVM arguments
for (String string : _jvmargs) {
args.add(processArg(string));
if (j > -1) {
ext = filename.substring(j+1);
}
- if (ext != null && LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase())) {
+ if (ext != null && LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase(Locale.ROOT))) {
// this file extension should have been dealt with in Getdown class
} else {
_appargs.add(0, "-open");
for (String string : _appargs) {
args.add(processArg(string));
}
-
+
String[] envp = createEnvironment();
String[] sargs = args.toArray(new String[args.size()]);
log.info("Running " + StringUtil.join(sargs, "\n "));
- return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+ // don't set the working dir, leave it the same as the working dir of the invocation
+ //return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+ return Runtime.getRuntime().exec(sargs, envp);
}
/**
clearValidationMarkers();
// if the new copy validates, reinitialize ourselves; otherwise report baffling hoseage
if (_digest.validateResource(crsrc, null)) {
+ // unset _initialisedConfig so new file is initialised
+ _initialisedConfig = null;
init(true);
} else {
log.warning(CONFIG_FILE + " failed to validate even after redownloading. " +
String locatorFilename = filenames.length >= 1 ? filenames[0] : null;
if (
!StringUtil.isBlank(locatorFilename)
- && locatorFilename.toLowerCase().endsWith("."+Application.LOCATOR_FILE_EXTENSION)
+ && locatorFilename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)
) {
setLocatorFile(locatorFilename);
// remove the locator filename from the filenames array
for (int i = 0; i < filenames.length; i++) {
String filename = filenames[i];
// skip any other locator files in a multiple file list
- if (! filename.toLowerCase().endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
+ if (filename.startsWith("jalview://") || filename.startsWith("jalviews://")) {
+ setJalviewUri(filename);
+ } else if (! filename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
addStartupFile(filename);
}
}
_startupFiles.add(new File(filename));
}
+ public static void setJalviewUri(String uri) {
+ _jalviewUri = uri;
+ }
+
private Config createLocatorConfig(Config.ParseOpts opts) {
if (_locatorFile == null) {
return null;
protected static File _locatorFile;
protected static List<File> _startupFiles = new ArrayList<>();
+ protected static String _jalviewUri;
public static final String LOCATOR_FILE_EXTENSION = "jvl";
private boolean _initialised = false;
private Config _initialisedConfig = null;
+
+ public static String i4jVersion = null;
+ private String jvmmempc = null;
+ private String jvmmemmax = null;
}
git://source.jalview.org / jalview.git / blobdiff