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 jalview.bin.HiDPISetting;
import jalview.bin.MemorySetting;
+import jalview.util.HttpUtils;
import jalview.util.LaunchUtils;
import com.threerings.getdown.util.*;
}
}
- // test for jalview/s URL. Insert startupNotification URI into start of _appargs
+ // test for jalviewX://... URI. Insert startupNotification URI into start of _appargs
if (! StringUtil.isBlank(_jalviewUri)) {
_appargs.add(0, _jalviewUri);
}
+ /* don't convert jalviewX:// URIs to https:// URLs as Jalview can now do that
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);
+ String jalviewUri = _appargs.get(0);
+ log.info("Trying to parse uri '"+jalviewUri+"'");
+ if (HttpUtils.isJalviewSchemeUri(jalviewUri)) {
+ String jalviewUrl = HttpUtils.equivalentJalviewUrl(jalviewUri);
+ log.info("Turned url '"+jalviewUri+"' into '"+jalviewUrl+"'");
+ _appargs.clear();
+ _appargs.add(jalviewUrl);
}
}
+ */
for (String argString: _appargs) {
if (argString.startsWith("-jvmmempc=")) {
jvmmemmax = argString.substring(11);
continue;
}
+ if (argString.startsWith("--jvmmempc=")) {
+ jvmmempc = argString.substring(11);
+ continue;
+ }
+ if (argString.startsWith("--jvmmemmax=")) {
+ jvmmemmax = argString.substring(12);
+ continue;
+ }
}
// use saved preferences if no cmdline args
}
// almost finally check the startup file arguments
- for (File f : _startupFiles) {
- _appargs.add(f.getAbsolutePath());
- break; // Only add one file to open
+ for (String f : _startupFiles) {
+ _appargs.add(HttpUtils.isPlausibleUri(f)?f:new File(f).getAbsolutePath());
}
// check if one arg with recognised extension
}
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");
}
}
{
return new File(appdir, path);
}
-
- public static void setStartupFilesFromParameterString(String p) {
+
+ public static void setStartupFilesFromParameters(List<String> parameters) {
// multiple files *might* be passed in as space separated quoted filenames
String q = "\"";
- if (!StringUtil.isBlank(p)) {
- String[] filenames;
- // split quoted params or treat as single string array
- if (p.startsWith(q) && p.endsWith(q)) {
- // this fails if, e.g.
- // p=q("stupidfilename\" " "otherfilename")
- // let's hope no-one ever ends a filename with '" '
- filenames = p.substring(q.length(),p.length()-q.length()).split(q+" "+q);
- } else {
- // single unquoted filename
- filenames = new String[]{p};
- }
-
- // check for locator file. Only allow one locator file to be double clicked (if multiple files opened, ignore locator files)
- String locatorFilename = filenames.length >= 1 ? filenames[0] : null;
- if (
- !StringUtil.isBlank(locatorFilename)
- && locatorFilename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)
- ) {
- setLocatorFile(locatorFilename);
- // remove the locator filename from the filenames array
- String[] otherFilenames = new String[filenames.length - 1];
- System.arraycopy(filenames, 1, otherFilenames, 0, otherFilenames.length);
- filenames = otherFilenames;
- }
-
- for (int i = 0; i < filenames.length; i++) {
- String filename = filenames[i];
- // skip any other locator files in a multiple file list
- if (filename.startsWith("jalview://") || filename.startsWith("jalviews://")) {
- setJalviewUri(filename);
- } else if (! filename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
+ for (String p: parameters) {
+ if (!StringUtil.isBlank(p)) {
+ String filename;
+ // split quoted params or treat as single string array
+ if (p.startsWith(q) && p.endsWith(q)) {
+ filename = p.substring(q.length(),p.length()-q.length());
+ } else {
+ // single unquoted filename
+ filename = p;
+ }
+
+ /* Now letting Jalview convert these URIs.
+ // convert jalviewX://... URLs
+ if (HttpUtils.isJalviewSchemeUri(filename)) {
+ filename = HttpUtils.equivalentJalviewUrl(filename);
+ }
+ */
+
+ // check for locator file. Only allow one locator file to be double clicked (if multiple files opened, ignore locator files)
+ if (filename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
+ // convert jalviewX://... JVL files
+ setLocatorFile(HttpUtils.equivalentJalviewUrl(filename));
+ } else {
+ // skip any other locator files in a multiple file list
addStartupFile(filename);
}
}
}
}
-
+
+ public static String getStartupFilesParameterString(List<String> parameters, boolean changeJalviewSchemeUris) {
+ StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for(String f : parameters) {
+ if (first) {
+ first = false;
+ } else {
+ sb.append(' ');
+ }
+ String p = changeJalviewSchemeUris ? HttpUtils.equivalentJalviewUrl(f) : f;
+ if (p.contains(" ")) {
+ sb.append('"');
+ sb.append(p);
+ sb.append('"');
+ } else {
+ sb.append(p);
+ }
+ }
+ return sb.toString();
+ }
+
public static void setLocatorFile(String filename) {
- _locatorFile = new File(filename);
+ _locatorFile = filename;
}
public static void addStartupFile(String filename) {
- _startupFiles.add(new File(filename));
+ _startupFiles.add(filename);
}
public static void setJalviewUri(String uri) {
try {
Config tmpConfig = null;
Map<String, Object> tmpData = new HashMap<>();
- if (_locatorFile.exists()) {
- tmpConfig = Config.parseConfig(_locatorFile, opts);
+ if (HttpUtils.startsWithHttpOrHttps(_locatorFile)) {
+ URL locatorUrl = new URL(_locatorFile);
+ try (InputStream in = ConnectionUtil.open(proxy, locatorUrl, 0, 0).getInputStream();
+ InputStreamReader reader = new InputStreamReader(in, UTF_8);
+ BufferedReader bin = new BufferedReader(reader)) {
+ tmpConfig = Config.parseConfig(bin, opts);
+ }
+ } else if (new File(_locatorFile).exists()) {
+ tmpConfig = Config.parseConfig(new File(_locatorFile), opts);
+ }
+ if (tmpConfig != null) {
// appbase is sanitised in HostWhitelist
Map<String, Object> tmpConfigData = tmpConfig.getData();
if (tmpConfig != null) {
protected static final String ENV_VAR_PREFIX = "%ENV.";
protected static final Pattern ENV_VAR_PATTERN = Pattern.compile("%ENV\\.(.*?)%");
- protected static File _locatorFile;
- protected static List<File> _startupFiles = new ArrayList<>();
+ protected static String _locatorFile;
+ protected static List<String> _startupFiles = new ArrayList<>();
protected static String _jalviewUri;
public static final String LOCATOR_FILE_EXTENSION = "jvl";
git://source.jalview.org / jalview.git / blobdiff