JAL-2422 Fixed URL encoding of REST calls (broken paths in Windows due to colon)

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index d7e7937..812bfea 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -38,6 +38,9 @@ import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -363,7 +366,7 @@ public class ChimeraManager
    * Select something in Chimera
    * 
    * @param command
-   *          the selection command to pass to Chimera
+   *                  the selection command to pass to Chimera
    */
   public void select(String command)
   {
@@ -509,8 +512,8 @@ public class ChimeraManager
 
   /**
    * Return the list of depiction presets available from within Chimera. Chimera
-   * will return the list as a series of lines with the format: Preset type
-   * number "description"
+   * will return the list as a series of lines with the format: Preset type number
+   * "description"
    * 
    * @return list of presets
    */
@@ -551,9 +554,9 @@ public class ChimeraManager
   }
 
   /**
-   * Launch Chimera, unless an instance linked to this object is already
-   * running. Returns true if chimera is successfully launched, or already
-   * running, else false.
+   * Launch Chimera, unless an instance linked to this object is already running.
+   * Returns true if chimera is successfully launched, or already running, else
+   * false.
    * 
    * @param chimeraPaths
    * @return
@@ -696,7 +699,7 @@ public class ChimeraManager
    * Determine the color that Chimera is using for this model.
    * 
    * @param model
-   *          the ChimeraModel we want to get the Color for
+   *                the ChimeraModel we want to get the Color for
    * @return the default model Color for this model in Chimera
    */
   public Color getModelColor(ChimeraModel model)
@@ -713,11 +716,11 @@ public class ChimeraManager
   /**
    * 
    * Get information about the residues associated with a model. This uses the
-   * Chimera listr command. We don't return the resulting residues, but we add
-   * the residues to the model.
+   * Chimera listr command. We don't return the resulting residues, but we add the
+   * residues to the model.
    * 
    * @param model
-   *          the ChimeraModel to get residue information for
+   *                the ChimeraModel to get residue information for
    * 
    */
   public void addResidues(ChimeraModel model)
@@ -809,10 +812,10 @@ public class ChimeraManager
    * Send a command to Chimera.
    * 
    * @param command
-   *          Command string to be send.
+   *                  Command string to be send.
    * @param reply
-   *          Flag indicating whether the method should return the reply from
-   *          Chimera or not.
+   *                  Flag indicating whether the method should return the reply
+   *                  from Chimera or not.
    * @return List of Strings corresponding to the lines in the Chimera reply or
    *         <code>null</code>.
    */
@@ -833,7 +836,7 @@ public class ChimeraManager
      */
     int waited = 0;
     int pause = 25;
-    while (busy  && waited < 1001)
+    while (busy && waited < 1001)
     {
       try
       {
@@ -876,8 +879,16 @@ public class ChimeraManager
     String method = getHttpRequestMethod();
     if ("GET".equals(method))
     {
-      command = command.replace(" ", "+").replace("#", "%23")
-              .replace("|", "%7C").replace(";", "%3B");
+      try
+      {
+        command = URLEncoder.encode(command,
+                StandardCharsets.UTF_8.toString());
+      } catch (UnsupportedEncodingException e)
+      {
+        command = command.replace(" ", "+").replace("#", "%23")
+                .replace("|", "%7C").replace(";", "%3B")
+                .replace(":", "%3A");
+      }
     }
     commands.add(new BasicNameValuePair("command", command));