From f0efe3029537bbbbe788e16eb85cb0af9c0fb81e Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 23 Jul 2018 11:28:58 +0100
Subject: [PATCH] JAL-3070 pushed down JABAWS specific args for
 WsJobParameters to Jws2Client

---
 src/jalview/gui/WsJobParameters.java   |  273 +-------------------------------
 src/jalview/ws/jws2/Jws2Client.java    |    5 +-
 test/jalview/ws/gui/Jws2ParamView.java |    4 +-
 3 files changed, 12 insertions(+), 270 deletions(-)

diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index 70e39b4..f2c4e96 100644
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -23,9 +23,6 @@ package jalview.gui;
 import jalview.gui.OptsAndParamsPage.OptionBox;
 import jalview.gui.OptsAndParamsPage.ParamBox;
 import jalview.util.MessageManager;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.OptionI;
@@ -48,17 +45,13 @@ import java.awt.event.HierarchyBoundsListener;
 import java.awt.event.HierarchyEvent;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
-import java.awt.event.WindowEvent;
-import java.awt.event.WindowListener;
 import java.util.Hashtable;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JButton;
 import javax.swing.JComboBox;
 import javax.swing.JDialog;
-import javax.swing.JFrame;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
@@ -67,11 +60,6 @@ import javax.swing.border.TitledBorder;
 import javax.swing.event.DocumentEvent;
 import javax.swing.event.DocumentListener;
 
-import compbio.metadata.Argument;
-import compbio.metadata.Option;
-import compbio.metadata.Parameter;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
 import net.miginfocom.swing.MigLayout;
 
 /**
@@ -183,7 +171,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
    * @param jobArgset
    */
   public WsJobParameters(ParamDatastoreI paramStorei, Jws2Instance service,
-          WsParamSetI preset, List<Argument> jobArgset)
+          WsParamSetI preset, List<ArgumentI> jobArgset)
   {
     super();
 
@@ -506,19 +494,11 @@ public class WsJobParameters extends JPanel implements ItemListener,
     }
   }
 
-  void initForService(WsParamSetI jabap, List<Argument> jabajobArgset)
+  void initForService(WsParamSetI paramSet, List<ArgumentI> jobArgset)
   {
-    WsParamSetI p = null;
-    List<ArgumentI> jobArgset = null;
     settingDialog = true;
-    { // instantiate the abstract proxy for Jaba objects
-      jobArgset = jabajobArgset == null ? null
-              : JabaParamStore.getJwsArgsfromJaba(jabajobArgset);
-      p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
-                 // null;
-    }
 
-    init(p, jobArgset);
+    init(paramSet, jobArgset);
 
   }
 
@@ -927,243 +907,6 @@ public class WsJobParameters extends JPanel implements ItemListener,
     revalidate();
   }
 
-  /**
-   * testing method - grab a service and parameter set and show the window
-   * 
-   * @param args
-   */
-  public static void main(String[] args)
-  {
-    jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
-            .getDiscoverer();
-    int p = 0;
-    if (args.length > 0)
-    {
-      Vector<String> services = new Vector<>();
-      services.addElement(args[p++]);
-      Jws2Discoverer.getDiscoverer().setServiceUrls(services);
-    }
-    try
-    {
-      disc.run();
-    } catch (Exception e)
-    {
-      System.err.println("Aborting. Problem discovering services.");
-      e.printStackTrace();
-      return;
-    }
-    Jws2Instance lastserv = null;
-    for (Jws2Instance service : disc.getServices())
-    {
-      lastserv = service;
-      if (p >= args.length || service.getName().equalsIgnoreCase(args[p]))
-      {
-        if (lastserv != null)
-        {
-          List<Preset> prl = null;
-          Preset pr = null;
-          if (++p < args.length)
-          {
-            PresetManager prman = lastserv.getPresets();
-            if (prman != null)
-            {
-              pr = prman.getPresetByName(args[p]);
-              if (pr == null)
-              {
-                // just grab the last preset.
-                prl = prman.getPresets();
-              }
-            }
-          }
-          else
-          {
-            PresetManager prman = lastserv.getPresets();
-            if (prman != null)
-            {
-              prl = prman.getPresets();
-            }
-          }
-          Iterator<Preset> en = (prl == null) ? null : prl.iterator();
-          while (en != null && en.hasNext())
-          {
-            if (en != null)
-            {
-              if (!en.hasNext())
-              {
-                en = prl.iterator();
-              }
-              pr = en.next();
-            }
-            {
-              System.out.println("Testing opts dupes for "
-                      + lastserv.getUri() + " : " + lastserv.getActionText()
-                      + ":" + pr.getName());
-              List<Option> rg = lastserv.getRunnerConfig().getOptions();
-              for (Option o : rg)
-              {
-                try
-                {
-                  Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
-                } catch (Exception e)
-                {
-                  System.err.println("Failed to copy " + o.getName());
-                  e.printStackTrace();
-                } catch (Error e)
-                {
-                  System.err.println("Failed to copy " + o.getName());
-                  e.printStackTrace();
-                }
-              }
-            }
-            {
-              System.out.println("Testing param dupes:");
-              List<Parameter> rg = lastserv.getRunnerConfig()
-                      .getParameters();
-              for (Parameter o : rg)
-              {
-                try
-                {
-                  Parameter cpy = jalview.ws.jws2.ParameterUtils
-                          .copyParameter(o);
-                } catch (Exception e)
-                {
-                  System.err.println("Failed to copy " + o.getName());
-                  e.printStackTrace();
-                } catch (Error e)
-                {
-                  System.err.println("Failed to copy " + o.getName());
-                  e.printStackTrace();
-                }
-              }
-            }
-            {
-              System.out.println("Testing param write:");
-              List<String> writeparam = null, readparam = null;
-              try
-              {
-                writeparam = jalview.ws.jws2.ParameterUtils
-                        .writeParameterSet(
-                                pr.getArguments(lastserv.getRunnerConfig()),
-                                " ");
-                System.out.println("Testing param read :");
-                List<Option> pset = jalview.ws.jws2.ParameterUtils
-                        .processParameters(writeparam,
-                                lastserv.getRunnerConfig(), " ");
-                readparam = jalview.ws.jws2.ParameterUtils
-                        .writeParameterSet(pset, " ");
-                Iterator<String> o = pr.getOptions().iterator(),
-                        s = writeparam.iterator(), t = readparam.iterator();
-                boolean failed = false;
-                while (s.hasNext() && t.hasNext())
-                {
-                  String on = o.next(), sn = s.next(), st = t.next();
-                  if (!sn.equals(st))
-                  {
-                    System.out.println(
-                            "Original was " + on + " Phase 1 wrote " + sn
-                                    + "\tPhase 2 wrote " + st);
-                    failed = true;
-                  }
-                }
-                if (failed)
-                {
-                  System.out.println(
-                          "Original parameters:\n" + pr.getOptions());
-                  System.out.println(
-                          "Wrote parameters in first set:\n" + writeparam);
-                  System.out.println(
-                          "Wrote parameters in second set:\n" + readparam);
-
-                }
-              } catch (Exception e)
-              {
-                e.printStackTrace();
-              }
-            }
-            WsJobParameters pgui = new WsJobParameters(null, lastserv,
-                    new JabaPreset(lastserv, pr), null);
-            JFrame jf = new JFrame(MessageManager
-                    .formatMessage("label.ws_parameters_for", new String[]
-                    { lastserv.getActionText() }));
-            JPanel cont = new JPanel(new BorderLayout());
-            pgui.validate();
-            cont.setPreferredSize(pgui.getPreferredSize());
-            cont.add(pgui, BorderLayout.CENTER);
-            jf.setLayout(new BorderLayout());
-            jf.add(cont, BorderLayout.CENTER);
-            jf.validate();
-            final Thread thr = Thread.currentThread();
-            jf.addWindowListener(new WindowListener()
-            {
-
-              @Override
-              public void windowActivated(WindowEvent e)
-              {
-                // TODO Auto-generated method stub
-
-              }
-
-              @Override
-              public void windowClosed(WindowEvent e)
-              {
-              }
-
-              @Override
-              public void windowClosing(WindowEvent e)
-              {
-                thr.interrupt();
-
-              }
-
-              @Override
-              public void windowDeactivated(WindowEvent e)
-              {
-                // TODO Auto-generated method stub
-
-              }
-
-              @Override
-              public void windowDeiconified(WindowEvent e)
-              {
-                // TODO Auto-generated method stub
-
-              }
-
-              @Override
-              public void windowIconified(WindowEvent e)
-              {
-                // TODO Auto-generated method stub
-
-              }
-
-              @Override
-              public void windowOpened(WindowEvent e)
-              {
-                // TODO Auto-generated method stub
-
-              }
-
-            });
-            jf.setVisible(true);
-            boolean inter = false;
-            while (!inter)
-            {
-              try
-              {
-                Thread.sleep(10000);
-              } catch (Exception e)
-              {
-                inter = true;
-              }
-              ;
-            }
-            jf.dispose();
-          }
-        }
-      }
-    }
-  }
-
   public boolean isServiceDefaults()
   {
     return (!isModified()
@@ -1296,6 +1039,10 @@ public class WsJobParameters extends JPanel implements ItemListener,
    */
   protected void updateWebServiceMenus()
   {
+    if (Desktop.instance == null)
+    {
+      return;
+    }
     for (AlignFrame alignFrame : Desktop.getAlignFrames())
     {
       alignFrame.BuildWebServiceMenu();
@@ -1368,12 +1115,6 @@ public class WsJobParameters extends JPanel implements ItemListener,
 
   }
 
-  private void _renameExistingPreset(String oldName, String curSetName2)
-  {
-    paramStore.updatePreset(oldName, curSetName2, setDescr.getText(),
-            getJobParams());
-  }
-
   /**
    * store current settings as given name. You should then reset gui.
    * 
diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java
index 3e4cc97..dfa7598 100644
--- a/src/jalview/ws/jws2/Jws2Client.java
+++ b/src/jalview/ws/jws2/Jws2Client.java
@@ -32,6 +32,7 @@ import jalview.ws.api.UIinfo;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.dm.JabaWsParamSet;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
@@ -112,10 +113,10 @@ public abstract class Jws2Client extends jalview.ws.WSClient
               && paramset.size() > 0)
                       ? new WsJobParameters((ParamDatastoreI) null, sh,
                               (WsParamSetI) null,
-                              paramset)
+                              JabaParamStore.getJwsArgsfromJaba(paramset))
                       : new WsJobParameters((ParamDatastoreI) null, sh,
                               preset,
-                              (List<Argument>) null);
+                              (List<ArgumentI>) null);
       if (adjustingExisting)
       {
         jobParams.setName(MessageManager
diff --git a/test/jalview/ws/gui/Jws2ParamView.java b/test/jalview/ws/gui/Jws2ParamView.java
index b56c10c..428f263 100644
--- a/test/jalview/ws/gui/Jws2ParamView.java
+++ b/test/jalview/ws/gui/Jws2ParamView.java
@@ -28,6 +28,7 @@ import jalview.ws.jabaws.JalviewJabawsTestUtils;
 import jalview.ws.jws2.JabaPreset;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
 import jalview.ws.params.ParamDatastoreI;
 
 import java.awt.BorderLayout;
@@ -43,7 +44,6 @@ import javax.swing.JPanel;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-import compbio.metadata.Argument;
 import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 
@@ -131,7 +131,7 @@ public class Jws2ParamView
           }
           WsJobParameters pgui = new WsJobParameters((ParamDatastoreI) null,
                   service, new JabaPreset(service, pr),
-                  (List<Argument>) null);
+                  (List<ArgumentI>) null);
           JFrame jf = new JFrame(MessageManager
                   .formatMessage("label.ws_parameters_for", new String[]
                   { service.getActionText() }));
-- 
1.7.10.2