From 822aa88e5d60d4e37e9776924ab993000bf821c9 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 24 Jan 2024 16:11:35 +0000
Subject: [PATCH] JAL-4374 source changes for getdown to clone URI and change
 scheme. Also added jalview://relativepath/...

---
 .../com/threerings/getdown/data/Application.java   |   34 ++++++++++++--------
 1 file changed, 21 insertions(+), 13 deletions(-)

diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
index 435ebbd..83a10ed 100644
--- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
+++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
@@ -1129,24 +1129,29 @@ public class Application
             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();
-                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() : "")
+                if (host.equals("relativepath") && file != null && file.startsWith("/") && !file.contains("/../")) {
+                  // remove 'URI-necessary' leading slash if host is 'relativepath'
+                  // but don't allow relative paths with a '..' folder in it.
+                  file = file.substring(1);
+                  _appargs.add(file);
+                } else if (host != null && host.length() > 0) {
+                  boolean https = jalviewUri.getScheme().equals("jalviews");
+                  URI httpUri = new URI(
+                          https?"https":"http",
+                          jalviewUri.getUserInfo(),
+                          jalviewUri.getHost(),
+                          jalviewUri.getPort(),
+                          jalviewUri.getPath(),
+                          jalviewUri.getQuery(),
+                          jalviewUri.getFragment()
                           );
-                  _appargs.add(newUrl.toString());
+                  _appargs.add(httpUri.toASCIIString());
                 } else {
                   _appargs.add(file);
                 }
@@ -1156,16 +1161,19 @@ public class Application
                   for (String refArg : refArgs) {
                     if (refArg.startsWith("jvmmempc=")) {
                       jvmmempc = refArg.substring(9);
+                      log.info("Found 'jvmmempc' arg '"+refArg+"'");
                       continue;
                     }
                     if (refArg.startsWith("jvmmemmax=")) {
                       jvmmemmax = refArg.substring(10);
+                      log.info("Found 'jvmmemmax' arg '"+refArg+"'");
                       continue;
                     }
-                    _appargs.add(URLDecoder.decode(refArg, "UTF-8"));
+                    String arg = URLDecoder.decode(refArg, "UTF-8");
+                    log.info("Adding apparg '"+arg+"'");
+                    _appargs.add(arg);
                   }
                 }
-                
               }
             }
           } catch (URISyntaxException e) {
-- 
1.7.10.2