Changeset 5714

Timestamp:

Sep 5, 2011, 2:10:42 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #1604: Support for multiple files of the same type in a FileSet?

The GUI can now be used to add multiple files of types that has enabled this.

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/FileSet.java (modified) (2 diffs)
• www/common/datafiles/select_files.jsp (modified) (16 diffs)
• www/include/scripts/main.js (modified) (1 diff)
• www/include/scripts/platforms.js (modified) (1 diff)
• www/include/scripts/table.js (modified) (1 diff)
• www/lims/arraydesigns/edit_design.jsp (modified) (2 diffs)
• www/views/derivedbioassays/edit_bioassay.jsp (modified) (1 diff)
• www/views/rawbioassays/edit_rawbioassay.jsp (modified) (1 diff)

trunk/src/clients/web/net/sf/basedb/clients/web/Base.java

@@ -32 +32 @@
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.FileSet;
-import net.sf.basedb.core.FileSetMember;
 import net.sf.basedb.core.FileStoreEnabled;
 import net.sf.basedb.core.ItemSubtype;
 import net.sf.basedb.core.Location;
-import net.sf.basedb.core.Path;
 import net.sf.basedb.core.Platform;
 import net.sf.basedb.core.PlatformVariant;
@@ -1466 +1464 @@
     {
       String param = names.nextElement();
-      if (param.startsWith("datafile."))
-      {
-        /*
-        int dataFileTypeId = Values.getInt(param.substring(9));
-        DataFileType dft = DataFileType.getById(dc, dataFileTypeId);
-        String filePath = Values.getStringOrNull(request.getParameter(param));
-        if (fileSet == null) fileSet = item.getFileSet();
-        if (filePath == null)
-        {
-          // TODO #1604
-//          fileSet.removeMember(dft);
-        }
-        else
-        {
-          File file = File.getByPath(dc, new Path(filePath, Path.Type.FILE), false);
-          fileSet.setMember(file, dft);
-          if (cc != null)
-          {
-            cc.setRecent(file, dft.getExternalId(), maxRecent);
-          }
-        }
-        */
-      }
-      else if (param.startsWith("setfile."))
+      if (param.startsWith("setfile."))
       {
         int dataFileTypeId = Values.getInt(param.substring(8));
@@ -1520 +1495 @@
       else if (param.startsWith("removefile."))
       {
-        FileSetMember member = FileSetMember.getById(dc, Values.getInt(request.getParameter(param)));
+        int dataFileTypeId = Values.getInt(param.substring(11));
+        Integer[] fileId = Values.getInt(request.getParameterValues(param));
+        DataFileType dft = DataFileType.getById(dc, dataFileTypeId);
         if (fileSet == null) fileSet = item.getFileSet();
-        fileSet.removeMember(member);
+        for (Integer id : fileId)
+        {
+          File file = File.getById(dc, id);
+          fileSet.removeMember(file, dft);
+        }
       }
     }
     if (validate)
     {
+      if (fileSet == null) fileSet = item.getFileSet();
       fileSet.validate(dc);
     }

trunk/src/core/net/sf/basedb/core/FileSet.java

@@ -444 +444 @@
   }
   
+  
+  /**
+    Remove a file as a member from the file set.
+    
+    @param file The file to remove
+    @param type The type of the file
+    @return TRUE if a member was removed, FALSE if not
+    @throws InvalidUseOfNullException If file or type is null
+    @throws PermissionDeniedException If the logged in user doesn't
+      have write permission for this file set 
+    @since 3.0
+  */
+  public boolean removeMember(File file, DataFileType type)
+  {
+    checkPermission(Permission.WRITE);
+    if (file == null) throw new InvalidUseOfNullException("file");
+    if (type == null) throw new InvalidUseOfNullException("type");
+      
+    DbControl dc = getDbControl();
+    int typeId = type.getId();
+    int fileId = file.getId();
+    Iterator<FileSetMemberData> it = getData().getMembers().iterator();
+    // Keep track of removed members so that we can invoke metadata extensions
+    List<ValidatingFileSetMember> removed = new ArrayList<ValidatingFileSetMember>();
+    while (it.hasNext())
+    {
+      FileSetMemberData member = it.next();
+      if (member.getDataFileType().getId() == typeId && member.getFile().getId() == fileId)
+      {
+        it.remove();
+        if (member.getId() > 0)
+        {
+          FileSetMember m = dc.getItem(FileSetMember.class, member);
+          dc.deleteItem(m);
+          removed.add(new ValidatingFileSetMember(m));
+        }
+      }
+    }
+    if (removed.size() > 0)
+    {
+      // Create context and invoke the extensions system
+      ExtensionsInvoker<ValidationAction> invoker = getInvoker(dc);
+      
+      // Reset the metadata
+      invoker.render(new ResetMetadataRenderer(removed));
+    }
+    return removed.size() > 0;
+  }
+
+  
   /**
     Remove all member files of the given type. 
@@ -469 +519 @@
       {
         it.remove();
-        FileSetMember m = dc.getItem(FileSetMember.class, member);
-        dc.deleteItem(m);
-        removed.add(new ValidatingFileSetMember(m));
+        if (member.getId() > 0)
+        {
+          FileSetMember m = dc.getItem(FileSetMember.class, member);
+          dc.deleteItem(m);
+          removed.add(new ValidatingFileSetMember(m));
+        }
       }
     }

trunk/www/common/datafiles/select_files.jsp

@@ -165 +165 @@
     {
       // IE.
-      div.onclick = hideVisibleRecentFilesDiv;
-    }
-
+      document.body.onclick = hideVisibleRecentFilesDiv;
+    }
   }
   
   var lastFileTypeId;
-  var updateCheckboxes = false;
-  function addFilesOnClick(fileTypeId, extension, updateCheck)
+  var lastHasValidator = false;
+  function addFilesOnClick(fileTypeId, extension, hasValidator)
   {
     var frm = document.forms['datafiles'];
-    updateCheckboxes = updateCheck;
     var url = '../../filemanager/index.jsp?ID=<%=ID%>&cmd=SelectMultiple&callback=addFileCallback';
     if (extension)
@@ -186 +184 @@
     }
     lastFileTypeId = fileTypeId;
+    lastHasValidator = hasValidator;
     Main.openPopup(url, 'SelectFile', 1000, 700);
   }
   function addFileCallback(fileId, path)
   {
-    addFile(lastFileTypeId, fileId, path);
-  }
-  function removeFilesOnClick(inputName, updateCheck)
-  {
-  }
-  
-  function browseOnClick(fileTypeId, extension, updateCheck)
+    addFile(lastFileTypeId, fileId, path, lastHasValidator);
+  }
+  
+  function browseOnClick(fileTypeId, extension, hasValidator)
   {
     var frm = document.forms['datafiles'];
-    updateCheckboxes = updateCheck;
     var url = '../../filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&callback=setFileCallback';
     if (extension)
@@ -210 +205 @@
     }
     lastFileTypeId = fileTypeId;
+    lastHasValidator = hasValidator;
     Main.openPopup(url, 'SelectFile', 1000, 700);
   }
   function setFileCallback(fileId, path)
   {
-    setFile(lastFileTypeId, fileId, path);
-  }
-  function setFile(fileTypeId, fileId, path)
+    setFile(lastFileTypeId, fileId, path, lastHasValidator);
+  }
+  function setFile(fileTypeId, fileId, path, hasValidator)
   {
     var frm = document.forms['datafiles'];
-    document.getElementById('filelist.'+fileTypeId+'.file').innerHTML = path;
+    var fileDiv = document.getElementById('filelist.'+fileTypeId+'.file');
+    if (fileId)
+    {
+      fileDiv.innerHTML = '<div id="filelist.'+fileTypeId+'.'+fileId+'">'+path+'</div>';
+    }
+    else
+    {
+      fileDiv.innerHTML = '';
+    }
+    if (hasValidator) frm['datafiles.validate'].checked = true;
     new FileAction('setfile', fileTypeId, fileId);
   }
-  function addFile(fileTypeId, fileId, path)
-  {
+  function addFile(fileTypeId, fileId, path, hasValidator)
+  {
+    var frm = document.forms['datafiles'];
     var fileDiv = document.getElementById('filelist.'+fileTypeId+'.'+fileId);
     if (fileDiv) return;
@@ -229 +235 @@
     fileDiv = document.createElement('div');
     fileDiv.id = 'filelist.'+fileTypeId+'.'+fileId;
-    fileDiv.innerHTML = path;
+    var html = path + '&nbsp;<img border=0 class="icon" style="cursor: pointer;" title="Remove this file" ';
+    html += ' onclick="removeFileOnClick(event, '+fileTypeId+','+fileId+','+hasValidator+')" src="/trunk/images/remove.png">';
+    fileDiv.innerHTML = html; 
     document.getElementById('filelist.'+fileTypeId+'.file').appendChild(fileDiv);
-    Main.hide('filelist.'+fileTypeId+'.0');
+    if (hasValidator) frm['datafiles.validate'].checked = true;
     new FileAction('addfile', fileTypeId, fileId);
   }
-  function removeOnClick(fileTypeId, updateCheck)
-  {
-    document.getElementById('filelist.'+fileTypeId+'.file').innerHTML = '<i>- not selected -</i>';
-    new FileAction('setfile', fileTypeId, 0);
-  }
-  
-  /*
-  function fileOnChange(inputName, updateCheckbox)
+  function removeFileOnClick(event, fileTypeId, fileId, hasValidator)
   {
     var frm = document.forms['datafiles'];
-    var validateCheckbox = frm['datafiles.validate'];
-
-    // Check boxes should be updated if the data file type 
-    //supports validation or metadata-extraction
-    if (updateCheckbox)
-    {
-      if (frm[inputName].value != '' || frm[inputName].length > 0)
-      {
-        // Data filetype supports validation
-        if (validateCheckbox)
-        {
-          if (validateCheckbox.disabled) validateCheckbox.disabled = false;  
-          validateCheckbox.checked = "1";
-        }
-      }
-    }   
-  }
-  */
-  
-  function writeFileActions()
-  {
-    Main.debug(fileActions.length, true);
-    for (var i = 0; i < fileActions.length; i++)
-    {
-      var action = fileActions[i];
-      Main.debug(action.action + ':' + action.fileTypeId + '='+action.fileId);
+    var fileDiv = document.getElementById('filelist.'+fileTypeId+'.'+fileId);
+    document.getElementById('filelist.'+fileTypeId+'.file').removeChild(fileDiv);
+    if (hasValidator) frm['datafiles.validate'].checked = true;
+    new FileAction('removefile', fileTypeId, fileId);
+    if (event.stopPropagation)
+    {
+      event.stopPropagation();
+    }
+    else
+    {
+      event.cancelBubble = true;
     }
   }
@@ -280 +266 @@
     this.fileId = fileId;
     
-    if (action == 'setfile')
-    {
-      for (var i = 0; i < fileActions.length; i++)
+
+    for (var i = fileActions.length-1; i >= 0; i--)
+    {
+      var other = fileActions[i];
+      
+      var remove = false;
+      if (action == 'setfile')
       {
-        var other = fileActions[i];
-        if (other.action == this.action && other.fileTypeId == this.fileTypeId)
-        {
-          fileActions[i] = this;
-          return;
-        }
+        // Remove all other actions for the given file type
+        remove = other.fileTypeId == this.fileTypeId;
       }
-      fileActions[fileActions.length] = this;
-    }
-    else if (action == 'addfile')
-    {
-      for (var i = 0; i < fileActions.length; i++)
+      else
       {
-        var other = fileActions[i];
-        if (other.action == this.action && other.fileTypeId == this.fileTypeId && other.fileId == this.fileId)
-        {
-          return;
-        }
+        // Remove all other actions for the given file type+file
+        remove = other.fileTypeId == this.fileTypeId && other.fileId == this.fileId;
       }
-      fileActions[fileActions.length] = this;
-    }
-  }
-  
-  function writeFileActionsToForm(frm)
-  {
-    alert(fileActions.length);
+      if (remove) fileActions.splice(i, 1);
+    }
+
+    fileActions[fileActions.length] = this;
+  }
+  
+  function writeFileActionsToForm(toForm)
+  {
+    var frm = document.forms['datafiles'];
+    Forms.createHidden(toForm, 'datafiles.validate', frm['datafiles.validate'].checked ? 1 : 0);
     for (var i = 0; i < fileActions.length; i++)
     {
       var action = fileActions[i];
-      Forms.createHidden(frm, action.action + '.' + action.fileTypeId, action.fileId);
+      Forms.createHidden(toForm, action.action + '.' + action.fileTypeId, action.fileId);
     }
   }
@@ -334 +316 @@
 
     visibleRecentFilesDiv = recentDiv;
-    event.cancelBubble = true;
-    event.stopPropagation();
-  }
-
-  function selectRecentFile(fileTypeId, fileId)
+    if (event.stopPropagation)
+    {
+      event.stopPropagation();
+    }
+    else
+    {
+      event.cancelBubble = true;
+    }
+  }
+
+  function selectRecentFile(fileTypeId, fileId, allowMultiple, hasValidator)
   {
     var path = document.getElementById('recentfile.'+fileTypeId+'.'+fileId).innerHTML;
-    setFile(fileTypeId, fileId, path);
+    if (allowMultiple)
+    {
+      addFile(fileTypeId, fileId, path, hasValidator);
+    }
+    else
+    {
+      setFile(fileTypeId, fileId, path, hasValidator);
+    }
   }
   
@@ -372 +367 @@
   }
   .filelist .file {
-    
+    cursor: pointer;
   }
   .filelist .required {
@@ -392 +387 @@
   .recentfiles .recentfile {
     padding: 2px;
-    border-bottom: 1px dotted #e0e0e0;
+    background: #f0f0f0;
+    border-bottom: 1px dotted #d0d0d0;
   }
   .recentfiles .recentfile:hover {
     cursor: pointer;
-    background: #e0e0e0;
+    background: #d0d0d0;
     padding: 2px;
+  }
+  .filelist .member {
+    xbackground: #ff0000;
   }
   </style>
@@ -406 +405 @@
     <div id="filelist" class="filelist" style="height: <%=(int)(scale*320)%>px; width:100%">
     <%
-    boolean hasNonPlatformFiles = true;     
+    boolean hasNonPlatformFiles = false;      
     boolean activateCheckBoxes = false;
-    boolean validationSupport = true;
+    boolean validationSupport = false;
     if (fileTypes.size() == 0)
     {
@@ -464 +463 @@
         String extension = dft.getExtension();
         boolean hasValidator = dft.hasActiveValidator(dc);
-        boolean affectCheckboxes = hasValidator;
         validationSupport |= hasValidator;
         List<FileSetMember> files = members.get(dft);
@@ -470 +468 @@
         %>
         <tr class="item <%=isRequired ? "required" : "" %>" 
-          id="filelist.<%=dftId%>" 
-          onclick="itemOnClick(<%=dftId%>)">
-          <td class="filetype" 
+          id="filelist.<%=dftId%>">
+          <td class="filetype" valign="top"
             id="filelist.<%=dftId%>.label"
             title="<%=fullLabel == label ? "" : HTML.encodeTags(fullLabel)%>"
@@ -481 +478 @@
               hasNonPlatformFiles = true;
               %>
-              <base:icon image="warning.gif" tooltip="This file is not part of the platform/subtype" />
+              <base:icon image="warning.gif" 
+                tooltip="This file is not part of the platform/subtype" />
               <%
             }
             %>
           </td>
-          <td class="file" id="filelist.<%=dftId%>.file">
+          <td class="file" id="filelist.<%=dftId%>.file" 
+            onclick="<%="recentFilesOnClick(event, " + dftId + ")"%>">
             <%
-            if (files == null || files.size() == 0)
-            {
-              %>
-              <div id="filelist.<%=dftId%>.0">
-              <i>- not selected -</i>
-              </div>
-              <%
-            }
-            else
+            if (files != null && files.size() > 0)
             {
               for (FileSetMember fm : files)
@@ -502 +493 @@
                 File file = fm.getFile();
                 %>
-                <div id="filelist.<%=dftId%>.<%=file.getId() %>">
+                <div id="filelist.<%=dftId%>.<%=file.getId()%>" class="member">
                 <%=file.getPath() %>
+                <base:icon image="remove.png" visible="<%=allowMultiple %>"
+                  tooltip="Remove this file"
+                  onclick="<%="removeFileOnClick(event, " + dftId + "," + file.getId() + "," + hasValidator + ")" %>"
+                />
                 </div>
                 <%
@@ -518 +513 @@
               onclick="<%="recentFilesOnClick(event, " + dftId + ")"%>"
             />
-              <div id="recentfiles.<%=dftId%>" style="display: none;" class="recentfiles">
+            <div id="recentfiles.<%=dftId%>" style="display: none;" class="recentfiles">
+              <div class="recentfile"
+                onclick="selectRecentFile(<%=dftId%>, 0, false, <%=hasValidator%>)"
+                id="recentfile.<%=dftId%>.0"
+                ><i>- clear -</i></div>
+              <%
+              for (File recent : recentFiles)
+              {
+                %>
                 <div class="recentfile"
-                  onclick="selectRecentFile(<%=dftId%>, 0)"
-                  id="recentfile.<%=dftId%>.0"
-                  ><i>- not selected -</i></div>
+                  onclick="selectRecentFile(<%=dftId%>, <%=recent.getId()%>, <%=allowMultiple ? 1 : 0 %>, <%=hasValidator%>)"
+                  id="recentfile.<%=dftId%>.<%=recent.getId()%>"
+                  ><%=HTML.encodeTags(recent.getPath().toString())%></div>
                 <%
-                for (File recent : recentFiles)
-                {
-                  %>
-                  <div class="recentfile"
-                    onclick="selectRecentFile(<%=dftId%>, <%=recent.getId()%>)"
-                    id="recentfile.<%=dftId%>.<%=recent.getId()%>"
-                    ><%=HTML.encodeTags(recent.getPath().toString())%></div>
-                  <%
-                }
-                %>
-              </div>
+              }
+              %>
+            </div>
           </td>
           <td class="fileaction">
             <base:icon image="add.png" 
-              onclick="<%="addFilesOnClick("+dftId+", '" + HTML.javaScriptEncode(extension) + "', "+ affectCheckboxes + ")"%>"
+              onclick="<%="addFilesOnClick("+dftId+", '" + HTML.javaScriptEncode(extension) + "', "+ hasValidator + ")"%>"
               visible="<%=allowMultiple %>"
             />
             <base:icon image="browse.png" 
-              onclick="<%="browseOnClick("+dftId+", '" + HTML.javaScriptEncode(extension) + "', "+ affectCheckboxes + ")"%>"
+              onclick="<%="browseOnClick("+dftId+", '" + HTML.javaScriptEncode(extension) + "', "+ hasValidator + ")"%>"
               visible="<%=!allowMultiple%>"
             />
           </td>
-          <!-- 
-          <td class="fileaction">
-            <base:icon image="remove.png" 
-              id="remove"
-              onclick="<%="removeOnClick("+dftId+", "+ affectCheckboxes + ")"%>"
-              visible="<%=!allowMultiple %>"
-            />
-          </td>
-          -->
         </tr>
         <%
@@ -573 +559 @@
           {
             %>
-            <b>Validate</b>
-            <input type="checkbox" value="1" disabled name="datafiles.validate">
+            <span title="Enabled this check box to validate and extract metadata from selected files">
+            <b>Validate files</b>
+            <input type="checkbox" value="1" name="datafiles.validate">
+            </span>
             <%
           }
@@ -606 +594 @@
       </table>
     </form>
-    <a href="javascript:writeFileActions()">See</a>
   </base:body>
   </base:page>

trunk/www/include/scripts/main.js

@@ -1981 +1981 @@
       // Only a single item in the list
       radio.checked = radio.value == value && !radio.disabled;
+      returnValue = 0;
     }
     return returnValue;

trunk/www/include/scripts/platforms.js

@@ -42 +42 @@
 
 
-  this.addDataFilesToForm = function(theFrame, frm)
-  {
-    var dataFilesFrm = theFrame.document.forms['datafiles'];
-    for (var i = 0; i < dataFilesFrm.length; i++)
-    {
-      var input = dataFilesFrm[i];
-      if (!input.disabled)
-      {
-        if (input.type == 'text')
-        {
-          Forms.createHidden(frm, input.name, input.value);
-        }
-        else if (input.type == 'checkbox')
-        {
-          Forms.createHidden(frm, input.name, input.checked ? input.value : '');
-        }
-      }
-    }
-  }
-  
   this.getPlatformById = function(id)
   {

trunk/www/include/scripts/table.js

@@ -418 +418 @@
     {
       var index = Forms.checkRadio(frm.item_id, itemId);
-      returnFunction(frm.item_id[index]);
+      returnFunction(frm.item_id.length ? frm.item_id[index] : frm.item_id);
     }
     else if (mode == 'selectmultiple' || mode == 'selectmultiplenobuttons')

trunk/www/lims/arraydesigns/edit_design.jsp

@@ -109 +109 @@
     catch (Throwable t)
     {}
-    if (currentPlatform == null && defaultPlatforms.size() > 0)
+    if (currentPlatform == null && defaultPlatforms != null && defaultPlatforms.size() > 0)
     {
       currentPlatform = defaultPlatforms.get(0);
     }
-    if (currentVariant == null && defaultVariants.size() > 0)
+    if (currentVariant == null && defaultVariants != null && defaultVariants.size() > 0)
     {
       currentVariant = defaultVariants.get(0);
@@ -199 +199 @@
         if (dataFilesLoaded)
         {
-          Platforms.addDataFilesToForm(frames.datafiles, frm);
+          frames.datafiles.writeFileActionsToForm(frm);
         }
         frm.submit();

trunk/www/views/derivedbioassays/edit_bioassay.jsp

@@ -297 +297 @@
         if (dataFilesLoaded)
         {
-          //Platforms.addDataFilesToForm(frames.datafiles, frm);
           frames.datafiles.writeFileActionsToForm(frm);
         }

trunk/www/views/rawbioassays/edit_rawbioassay.jsp

@@ -354 +354 @@
         if (dataFilesLoaded)
         {
-          Platforms.addDataFilesToForm(frames.datafiles, frm);
+          frames.datafiles.writeFileActionsToForm(frm);
         }
         frm.submit();