Changeset 3768

Timestamp:

Aug 17, 2010, 11:26:20 AM (13 years ago)

Author:

Gregory Vincic

Message:

Fixing #685. Multiple file selection now works. This commit also modifies the job name such that it states 'Mascot search: _name of parameter set_'. The TextField? class got a new constructor for easy construction with default value. HtmlTagWriter? was fixed so indentation works nicely. Action classes have been partly refactored aswell.

Location:

trunk

Files:

• api/waf/src/se/lu/thep/waf/HtmlTagWriter.java (modified) (4 diffs)
• client/servlet/src/org/proteios/action/mascot/SaveMascotParameterSetStorage.java (modified) (9 diffs)
• client/servlet/src/org/proteios/action/mascot/SearchMascot.java (modified) (1 diff)
• client/servlet/src/org/proteios/action/mascot/ViewActiveMascotParameterSetStorage.java (modified) (6 diffs)
• client/servlet/src/org/proteios/gui/form/TextField.java (modified) (1 diff)

trunk/api/waf/src/se/lu/thep/waf/HtmlTagWriter.java

@@ -74 +74 @@
   public void draw(Tag tag)
   {
+    indent++;
     if (tag instanceof CData)
     {
@@ -88 +89 @@
       for (Tag child : elements)
       {
-        indent++;
         child.draw(this);
       }
@@ -94 +94 @@
    {
       writeEndTag(writer, tag);
-      indent--;
    }
     }
+  indent--;
   }
 
@@ -113 +113 @@
           sb.append(">");
       else
-        sb.append("\n>");
+        sb.append(">\n");
   }
   else

trunk/client/servlet/src/org/proteios/action/mascot/SaveMascotParameterSetStorage.java

@@ -48 +48 @@
 import org.proteios.gui.Toolbar;
 import org.proteios.gui.form.Form;
+import org.proteios.gui.form.Fieldset;
+import org.proteios.gui.form.TextField;
 import org.proteios.gui.form.FormFactory;
 import org.proteios.gui.layout.RowLayout;
@@ -125 +127 @@
       throws ActionException, InvalidParameterValue
   {
-    /*
-     * Get the Mascot parameter set storage
-     */
-    log.debug("########## - Start");
-    //Integer mascotpssId = getSessionAttribute(ViewActiveMascotParameterSetStorage.VMASCOTPARAMETERSETSTORAGEID);
-    Integer mascotpssId = getValidInteger(ViewActiveMascotParameterSetStorage.VMASCOTPARAMETERSETSTORAGEID);
+
+  Integer mascotpssId;
+  Boolean saveMascotParameterSetFlag;
+  Boolean saveAsMascotParameterSetFlag;
+  Boolean useWebInterfaceFlag;
+  List<Integer> spectrumFileIds;
+  String forwardId, mascotSearchUserName, mascotSearchUserEmail, errorMessage, saveLabel;
+  DbControl dc;
+  ItemFactory factory;
+  MascotParameterSetStorage mascotpss;
+  MascotParameterSet mascotParameterSet;
+  Form form;
+  Toolbar tb;
+  RowLayout layout;
+  ActionLink action, forwardLink, saveAction;
+  // Define
+
+    mascotpssId = getValidInteger(ViewActiveMascotParameterSetStorage.VMASCOTPARAMETERSETSTORAGEID);
+    saveMascotParameterSetFlag = getValidBoolean(SearchMascot.VSAVEMASCOTPARAMETERSETFLAG);
+    saveAsMascotParameterSetFlag = getValidBoolean(SearchMascot.VSAVEASMASCOTPARAMETERSETFLAG);
+    forwardId = getValidString(FormFactory.VFWDACTION);
+    spectrumFileIds = getValidIntegerList(SearchMascot.VSPECTRUMFILEID);
+    useWebInterfaceFlag = getValidBoolean(SearchMascot.VMASCOTUSEWEBINTERFACEFLAG);
+  mascotSearchUserName = getValidString(SearchMascot.VMASCOT_SEARCH_USER_NAME);
+  mascotSearchUserEmail = getValidString(SearchMascot.VMASCOT_SEARCH_USER_EMAIL);
+
+    if (saveMascotParameterSetFlag == null) { saveMascotParameterSetFlag = false; }
+    if (saveAsMascotParameterSetFlag == null) { saveAsMascotParameterSetFlag = false; }
+
     log.debug("mascotParameterSetStorageId = " + mascotpssId);
-    // Get the save Mascot parameter set flag
-    Boolean saveMascotParameterSetFlag = getValidBoolean(SearchMascot.VSAVEMASCOTPARAMETERSETFLAG);
-    log.debug("saveMascotParameterSetFlag from request = " + saveMascotParameterSetFlag);
-    if (saveMascotParameterSetFlag == null)
-    {
-      saveMascotParameterSetFlag = false;
-    }
     log.debug("saveMascotParameterSetFlag = " + saveMascotParameterSetFlag);
-    // Get the "save as" Mascot parameter set flag
-    Boolean saveAsMascotParameterSetFlag = getValidBoolean(SearchMascot.VSAVEASMASCOTPARAMETERSETFLAG);
-    log.debug("saveAsMascotParameterSetFlag from request = " + saveAsMascotParameterSetFlag);
-    if (saveAsMascotParameterSetFlag == null)
-    {
-      saveAsMascotParameterSetFlag = false;
-    }
     log.debug("saveAsMascotParameterSetFlag = " + saveAsMascotParameterSetFlag);
-    String forwardId = getValidString(FormFactory.VFWDACTION);
-    // Get the forward id
     log.debug("forwardId = " + forwardId);
-    /*
-     * Get parameters that might need to be forwarded to next action
-     */
-    // Get the spectrum file items to use for the search
-    List<Integer> spectrumFileIds = getValidIntegerList(SearchMascot.VSPECTRUMFILEID);
     log.debug("spectrumFileIds = " + spectrumFileIds);
-    // Get the Mascot web interface flag
-    Boolean useWebInterfaceFlag = getValidBoolean(SearchMascot.VMASCOTUSEWEBINTERFACEFLAG);
-    log.debug("useWebInterfaceFlag from request = " + useWebInterfaceFlag);
-    // Get Mascot search user name
-    String mascotSearchUserName = getValidString(SearchMascot.VMASCOT_SEARCH_USER_NAME);
-    log.debug("mascotSearchUserName from request = \"" + mascotSearchUserName + "\"");
-    // Get Mascot search user email
-    String mascotSearchUserEmail = getValidString(SearchMascot.VMASCOT_SEARCH_USER_EMAIL);
-    log.debug("mascotSearchUserEmail from request = \"" + mascotSearchUserEmail + "\"");
-    //Integer eventId = getValidInteger(FormFactory.VID);
-    DbControl dc = newDbControl();
-    ItemFactory factory = getItemFactory(dc);
-    //UpdateEvent ue = factory.getById(UpdateEvent.class, eventId);
-    //MascotParameterSetStorage mascotpss = factory.getById(MascotParameterSetStorage.class, mascotpssId);
-    MascotParameterSetStorage mascotpss = null;
+  log.debug("useWebInterfaceFlag from request = " + useWebInterfaceFlag);
+  log.debug("mascotSearchUserName from request = \"" + mascotSearchUserName + "\"");
+  log.debug("mascotSearchUserEmail from request = \"" + mascotSearchUserEmail + "\"");
+  // Here
+    dc = newDbControl();
+    factory = getItemFactory(dc);
+    mascotpss = null;
     if (mascotpssId != null)
     {
@@ -177 +173 @@
     }
     // Fetch current Mascot parameter set from request
-    MascotParameterSet mascotParameterSet = fetchCurrentMascotParameterSet();
-    //
-    String errorMessage = null;
+    mascotParameterSet = fetchCurrentMascotParameterSet();
+    //
+    errorMessage = null;
     if (saveAsMascotParameterSetFlag)
     {
@@ -193 +189 @@
         log.debug("mascotpss.getParameterFile() = \"" + mascotpss.getParameterFile() + "\"");
         // MascotParameterSetStorage form
-        //Form form = getFormFactory().getSaveAsMascotParameterSetStorageForm(mascotParameterSetStorage, mascotParameterSet);
-        Form form = getFormFactory().getSaveAsMascotParameterSetStorageForm(mascotpss, mascotParameterSet);
+        form = getFormFactory().getSaveAsMascotParameterSetStorageForm(mascotpss, mascotParameterSet);
         // Toolbar
-        Toolbar tb = new Toolbar();
+        tb = new Toolbar();
         // Save button
-        String saveLabel = "Save";
-        ActionLink saveAction = getActionFactory().getActionLink(SaveMascotParameterSetStorage.class, saveLabel);
-        //saveAction.addParameter(ViewActiveMascotParameterSetStorage.VMASCOTPARAMETERSETSTORAGEID,
-        //  mascotpssId);
+        saveLabel = "Save";
+        saveAction = getActionFactory().getActionLink(SaveMascotParameterSetStorage.class, saveLabel);
         saveAction.addParameter(SearchMascot.VSAVEMASCOTPARAMETERSETFLAG,
           true);
@@ -212 +205 @@
           for (Integer spectrumFileId : spectrumFileIds)
           {
-            saveAction.addParameter(SearchMascot.VSPECTRUMFILEID, spectrumFileId);
+            form.getFieldsets().get(0).add(new TextField<Integer>(SearchMascot.VSPECTRUMFILEID, spectrumFileId).setHidden(true));
           }
         }
@@ -227 +220 @@
         form.setToolbar(tb);
         // Layout
-        RowLayout layout = getLayoutFactory().getRowLayout();
+        layout = getLayoutFactory().getRowLayout();
         layout.add(new Title("SaveAsMascotParameterSetStorage"));
         layout.add(form);
@@ -391 +384 @@
       // Return to "Save As..." form and display error message
       setError(errorMessage);
-      String saveLabel = "Save";
-      ActionLink action = getActionFactory().getActionLink(SaveMascotParameterSetStorage.class, saveLabel);
+      saveLabel = "Save";
+      action = getActionFactory().getActionLink(SaveMascotParameterSetStorage.class, saveLabel);
       setAttribute(SearchMascot.VSAVEMASCOTPARAMETERSETFLAG,
         false);
@@ -413 +406 @@
     {
       log.debug("forwardId != null, calling setForwardTo(forwardId = " + forwardId + ")");
-      ActionLink forwardLink = new ActionLink("forward",
+      forwardLink = new ActionLink("forward",
         forwardId);
       forwardLink.addParameter(ViewActiveMascotParameterSetStorage.VMASCOTPARAMETERSETSTORAGEID, mascotpssId);
@@ -434 +427 @@
     {
       log.debug("forwardId == null, calling setForwardTo(ViewActiveMascotParameterSetStorage.class)");
-      ActionLink forwardLink = getActionLink(ViewActiveMascotParameterSetStorage.class, "forward");
+      forwardLink = getActionLink(ViewActiveMascotParameterSetStorage.class, "forward");
       setForwardTo(forwardLink.getActionId());
     }

trunk/client/servlet/src/org/proteios/action/mascot/SearchMascot.java

@@ -270 +270 @@
       //job.setName(plugin.getName() + " File: " + file.getName());
       //job.setDescription("Gel: " + gelId + " File: " + file.getName());
-      job.setName(plugin.getName() + " Mascot Parameter Set: " + mascotpss.getName());
-      job.setDescription("Mascot Parameter Set: " + mascotpss.getName() + "[" + mascotpss.getId() + "] Spectrum File: " + spectrumFile.getName() + "[" + spectrumFile.getId() + "]");
+      job.setName("Mascot Search: " + mascotpss.getName());
+      job.setDescription("Mascot Parameter Set: " + mascotpss.getName() + "[" + mascotpss.getId() + "]\n Spectrum File: " + spectrumFile.getName() + "[" + spectrumFile.getId() + "]");
       //
       StringParameterType mascotWebServerURLStrParam = new StringParameterType();

trunk/client/servlet/src/org/proteios/action/mascot/ViewActiveMascotParameterSetStorage.java

@@ -37 +37 @@
 import org.proteios.gui.form.Form;
 import org.proteios.gui.form.FormFactory;
+import org.proteios.gui.form.Fieldset;
 import org.proteios.gui.form.Option;
+import org.proteios.gui.form.TextField;
 import org.proteios.gui.layout.RowLayout;
 import org.proteios.io.MascotParameterSet;
@@ -50 +52 @@
 
 /**
- * @author olle
+ * @author olle, gregory
  */
 public class ViewActiveMascotParameterSetStorage
@@ -108 +110 @@
   List<String> reportTopStringList;
   List<Option> reportTopOptionList;
+  Fieldset fs;
   // Define
 
@@ -218 +221 @@
      */
     toolbar = new Toolbar();
+  fs = mascotParameterSetForm.getFieldsets().get(0);
+  fs.add(new TextField<Integer>(VMASCOTPARAMETERSETSTORAGEID, mascotpssId).setHidden(true));
+  fs.add(new TextField<String>(SearchMascot.VMASCOT_SEARCH_USER_NAME, mascotSearchUserName).setHidden(true));
+  fs.add(new TextField<String>(SearchMascot.VMASCOT_SEARCH_USER_EMAIL, mascotSearchUserEmail).setHidden(true));
+
     if (spectrumFileIds == null)
     {
       // Save Mascot parameter set button
       save = getActionLink(SaveMascotParameterSetStorage.class, "Save");
-      save.addParameter(VMASCOTPARAMETERSETSTORAGEID, mascotpssId);
-      save.addParameter(SearchMascot.VMASCOT_SEARCH_USER_NAME, mascotSearchUserName);
-      save.addParameter(SearchMascot.VMASCOT_SEARCH_USER_EMAIL, mascotSearchUserEmail);
       save.addParameter(SearchMascot.VSAVEMASCOTPARAMETERSETFLAG, true);
       save.addParameter(FormFactory.VFWDACTION, ViewActiveMascotParameterSetStorage.class.getName());
@@ -230 +235 @@
       // "Save As" Mascot parameter set button
       saveAs = getActionLink(SaveMascotParameterSetStorage.class, "SaveAs");
-      saveAs.addParameter(VMASCOTPARAMETERSETSTORAGEID, mascotpssId);
-      saveAs.addParameter(SearchMascot.VMASCOT_SEARCH_USER_NAME, mascotSearchUserName);
-      saveAs.addParameter(SearchMascot.VMASCOT_SEARCH_USER_EMAIL, mascotSearchUserEmail);
       saveAs.addParameter(SearchMascot.VSAVEMASCOTPARAMETERSETFLAG, false);
       saveAs.addParameter(SearchMascot.VSAVEASMASCOTPARAMETERSETFLAG, true);
@@ -240 +242 @@
     else
     {
+   // Add file ids as hidden fields to the form
+      for (Integer spectrumFileId : spectrumFileIds)
+      {
+    TextField<Integer> hiddenFileField = new TextField<Integer>(SearchMascot.VSPECTRUMFILEID, spectrumFileId).setHidden(true);
+        fs.add(hiddenFileField);
+      }
+   fs.add(new TextField<Boolean>(SearchMascot.VMASCOTUSEWEBINTERFACEFLAG, useWebInterfaceFlag).setHidden(true));
       // Save and Search Mascot
       searchMascot = getActionLink(SaveMascotParameterSetStorage.class, "SaveAndSearchMascot");
-      searchMascot.addParameter(VMASCOTPARAMETERSETSTORAGEID, mascotpssId);
-      searchMascot.addParameter(SearchMascot.VMASCOT_SEARCH_USER_NAME, mascotSearchUserName);
-      searchMascot.addParameter(SearchMascot.VMASCOT_SEARCH_USER_EMAIL, mascotSearchUserEmail);
       searchMascot.addParameter(SearchMascot.VSAVEMASCOTPARAMETERSETFLAG, true);
       searchMascot.addParameter(FormFactory.VFWDACTION, SearchMascot.class.getName());
-      for (Integer spectrumFileId : spectrumFileIds)
-      {
-        searchMascot.addParameter(SearchMascot.VSPECTRUMFILEID, spectrumFileId);
-      }
-      searchMascot.addParameter(SearchMascot.VMASCOTUSEWEBINTERFACEFLAG, useWebInterfaceFlag);
       toolbar.add(searchMascot);
       // "Save As" and Search Mascot
       saveAsAndSearchMascot = getActionLink(SaveMascotParameterSetStorage.class, "SaveAsAndSearchMascot");
-      saveAsAndSearchMascot.addParameter(VMASCOTPARAMETERSETSTORAGEID, mascotpssId);
-      saveAsAndSearchMascot.addParameter(SearchMascot.VMASCOT_SEARCH_USER_NAME, mascotSearchUserName);
-      saveAsAndSearchMascot.addParameter(SearchMascot.VMASCOT_SEARCH_USER_EMAIL, mascotSearchUserEmail);
       saveAsAndSearchMascot.addParameter(SearchMascot.VSAVEMASCOTPARAMETERSETFLAG, false);
       saveAsAndSearchMascot.addParameter(SearchMascot.VSAVEASMASCOTPARAMETERSETFLAG, true);
       saveAsAndSearchMascot.addParameter(FormFactory.VFWDACTION, SearchMascot.class.getName());
-      for (Integer spectrumFileId : spectrumFileIds)
-      {
-        saveAsAndSearchMascot.addParameter(SearchMascot.VSPECTRUMFILEID, spectrumFileId);
-      }
-      saveAsAndSearchMascot.addParameter(SearchMascot.VMASCOTUSEWEBINTERFACEFLAG, useWebInterfaceFlag);
       toolbar.add(saveAsAndSearchMascot);
     }

trunk/client/servlet/src/org/proteios/gui/form/TextField.java

@@ -52 +52 @@
 
 
-  public TextField(VParameter vemail)
+  public TextField(VParameter vparam)
   {
-    super(vemail);
+    super(vparam);
+  }
+
+  public TextField(VParameter vparam, D value)
+  {
+    super(vparam);
+  setValue(value);
   }