From: Ben Soares <b.soares@dundee.ac.uk>
Date: Tue, 21 May 2024 14:55:57 +0000 (+0100)
Subject: JAL-4409 Make HttpUtils.equivalentJalviewUrlString 'non-destructive'
X-Git-Tag: Release_2_11_4_0~28^2~13
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dee97314c8d002df2ec57812bf82f0460ba51dd8;p=jalview.git

JAL-4409 Make HttpUtils.equivalentJalviewUrlString 'non-destructive'
---

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 05b987e..97ab98e 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -239,8 +239,6 @@ public class Commands
         String openFile0 = av.getValue();
         String openFile = HttpUtils.equivalentJalviewUrl(openFile0);
         if (openFile == null)
-          openFile = openFile0;
-        if (openFile == null)
           continue;
 
         theseArgsWereParsed = true;
diff --git a/src/jalview/util/ArgParserUtils.java b/src/jalview/util/ArgParserUtils.java
index be0f428..fabbc76 100644
--- a/src/jalview/util/ArgParserUtils.java
+++ b/src/jalview/util/ArgParserUtils.java
@@ -100,7 +100,8 @@ public class ArgParserUtils
             continue;
           }
           filenames.add(pos + 1, a.argString());
-          filenames.add(pos + 2, associatedFile);
+          filenames.add(pos + 2,
+                  HttpUtils.equivalentJalviewUrl(associatedFile));
         }
       }
       // add an --open arg to separate from other files
diff --git a/src/jalview/util/HttpUtils.java b/src/jalview/util/HttpUtils.java
index c3f32fc..04a820d 100644
--- a/src/jalview/util/HttpUtils.java
+++ b/src/jalview/util/HttpUtils.java
@@ -243,7 +243,8 @@ public class HttpUtils
   {
     if (!isJalviewSchemeUri(jalviewUriString))
     {
-      return null;
+      // not a jalviewUriString, hand it back
+      return jalviewUriString;
     }
     URI jalviewUri;
     try