From d30a1e3993c5538efdecd3149dc8e5a1e4e42936 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 28 Sep 2018 12:29:55 +0100
Subject: [PATCH] JAL-3063 service param files read/saved using JAXB not
 Castor binding

---
 src/jalview/gui/WsParamSetManager.java |   60 ++++++++++++++++++++++----------
 1 file changed, 41 insertions(+), 19 deletions(-)

diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java
index d91775c..cb98856 100644
--- a/src/jalview/gui/WsParamSetManager.java
+++ b/src/jalview/gui/WsParamSetManager.java
@@ -27,8 +27,11 @@ import jalview.util.MessageManager;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.ParamManager;
 import jalview.ws.params.WsParamSetI;
+import jalview.xml.binding.jalview.ObjectFactory;
+import jalview.xml.binding.jalview.WebServiceParameterSet;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
@@ -39,6 +42,12 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.StringTokenizer;
 
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
+
 /**
  * store and retrieve web service parameter sets.
  * 
@@ -47,7 +56,7 @@ import java.util.StringTokenizer;
  */
 public class WsParamSetManager implements ParamManager
 {
-  Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<String, ParamDatastoreI>();
+  Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<>();
 
   @Override
   public WsParamSetI[] getParameterSet(String name, String serviceUrl,
@@ -60,7 +69,7 @@ public class WsParamSetManager implements ParamManager
     }
     StringTokenizer st = new StringTokenizer(files, "|");
     String pfile = null;
-    ArrayList<WsParamSetI> params = new ArrayList<WsParamSetI>();
+    List<WsParamSetI> params = new ArrayList<>();
     while (st.hasMoreTokens())
     {
       pfile = st.nextToken();
@@ -107,33 +116,39 @@ public class WsParamSetManager implements ParamManager
 
   private WsParamSetI[] parseParamFile(String filename) throws IOException
   {
-    List<WsParamSetI> psets = new ArrayList<WsParamSetI>();
+    List<WsParamSetI> psets = new ArrayList<>();
     InputStreamReader is = new InputStreamReader(
-            new java.io.FileInputStream(new File(filename)), "UTF-8");
-
-    jalview.schemabinding.version2.WebServiceParameterSet wspset = new jalview.schemabinding.version2.WebServiceParameterSet();
+            new FileInputStream(new File(filename)), "UTF-8");
 
-    org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
-            wspset);
-    unmar.setWhitespacePreserve(true);
+    WebServiceParameterSet wspset = null;
     try
     {
-      wspset = (jalview.schemabinding.version2.WebServiceParameterSet) unmar
-              .unmarshal(is);
+      JAXBContext jc = JAXBContext
+              .newInstance("jalview.xml.binding.jalview");
+      javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+      XMLStreamReader streamReader = XMLInputFactory.newInstance()
+              .createXMLStreamReader(is);
+      JAXBElement<WebServiceParameterSet> jbe = um.unmarshal(streamReader,
+              WebServiceParameterSet.class);
+      wspset = jbe.getValue();
     } catch (Exception ex)
     {
       throw new IOException(ex);
     }
+
     if (wspset != null && wspset.getParameters().length() > 0)
     {
-      for (String url : wspset.getServiceURL())
+      List<String> urls = wspset.getServiceURL();
+      final String[] urlArray = urls.toArray(new String[urls.size()]);
+
+      for (String url : urls)
       {
         ParamDatastoreI parser = paramparsers.get(url);
         if (parser != null)
         {
           WsParamSetI pset = parser.parseServiceParameterFile(
                   wspset.getName(), wspset.getDescription(),
-                  wspset.getServiceURL(), wspset.getParameters());
+                  urlArray, wspset.getParameters());
           if (pset != null)
           {
             pset.setSourceFile(filename);
@@ -190,8 +205,7 @@ public class WsParamSetManager implements ParamManager
       if (value == JalviewFileChooser.APPROVE_OPTION)
       {
         outfile = chooser.getSelectedFile();
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                outfile.getParent());
+        Cache.setProperty("LAST_DIRECTORY", outfile.getParent());
         filename = outfile.getAbsolutePath();
         if (!filename.endsWith(".wsparams"))
         {
@@ -212,13 +226,16 @@ public class WsParamSetManager implements ParamManager
         }
         paramFiles = paramFiles.concat(filename);
       }
-      jalview.bin.Cache.setProperty("WS_PARAM_FILES", paramFiles);
+      Cache.setProperty("WS_PARAM_FILES", paramFiles);
 
-      jalview.schemabinding.version2.WebServiceParameterSet paramxml = new jalview.schemabinding.version2.WebServiceParameterSet();
+      WebServiceParameterSet paramxml = new WebServiceParameterSet();
 
       paramxml.setName(parameterSet.getName());
       paramxml.setDescription(parameterSet.getDescription());
-      paramxml.setServiceURL(parameterSet.getApplicableUrls().clone());
+      for (String url : parameterSet.getApplicableUrls())
+      {
+        paramxml.getServiceURL().add(url);
+      }
       paramxml.setVersion("1.0");
       try
       {
@@ -226,7 +243,12 @@ public class WsParamSetManager implements ParamManager
                 parser.generateServiceParameterFile(parameterSet));
         PrintWriter out = new PrintWriter(new OutputStreamWriter(
                 new FileOutputStream(outfile), "UTF-8"));
-        paramxml.marshal(out);
+        JAXBContext jaxbContext = JAXBContext
+                .newInstance(WebServiceParameterSet.class);
+        Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+        jaxbMarshaller.marshal(
+                new ObjectFactory().createWebServiceParameterSet(paramxml),
+                out);
         out.close();
         parameterSet.setSourceFile(filename);
       } catch (Exception e)
-- 
1.7.10.2