Changeset 8032

Timestamp:

Feb 1, 2022, 2:04:44 PM (20 months ago)

Author:

Nicklas Nordborg

Message:

Merge BASE 3.19.2 to the trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• credits.txt (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/batchimport/RawBioAssayImporter.java (modified) (5 diffs)
• www/admin/extensions/details.js (modified) (1 diff)
• www/admin/extensions/wizard.jsp (modified) (7 diffs)

trunk/credits.txt

@@ -1 +1 @@
 $Id$
 
-The current BASE team is (at BASE 3.19.1 release)
+The current BASE team is (at BASE 3.19.2 release)
 {{{
 Jari Häkkinen

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/RawBioAssayImporter.java

@@ -162 +162 @@
     );
 
-  
+  protected static final PluginParameter<String> fileSpotsMapping = 
+    new PluginParameter<String>(
+        "fileSpotsMapping",
+        "File spots",
+        "Mapping that picks the number of spots of the bioassay that are stored in files. The " +
+        "values must be in the numeric format specified by the 'Number format' parameter." +
+        "Example: \\Spots\\",
+        optionalColumnMapping
+    );
+
   public RawBioAssayImporter()
   {}
@@ -198 +207 @@
   private Mapper fileTypeMapper;
   private Mapper fileMapper;
+  private Mapper fileSpotsMapper;
   private String dataDirectory;
   
@@ -264 +274 @@
     parameters.add(fileTypeColumnMapping);
     parameters.add(fileColumnMapping);
+    parameters.add(fileSpotsMapping);
     parameters.add(permissionTemplateColumnMapping);
   }
@@ -297 +308 @@
     fileTypeMapper = getMapper(ffp, (String)job.getValue("fileTypeColumnMapping"), null, null);
     fileMapper = getMapper(ffp, (String)job.getValue("fileColumnMapping"), null, null);
+    fileSpotsMapper = getMapper(ffp, (String)job.getValue("fileSpotsMapping"), null, null);
     dataDirectory = (String)job.getValue("dataDirectory");
     if (dataDirectory != null && !dataDirectory.endsWith("/"))
@@ -390 +402 @@
       rba.setParentExtract(extractFromBioAssay);
     }
-    
+    if (fileSpotsMapper != null) rba.setNumFileSpots(fileSpotsMapper.getInt(data));
     if (!rba.hasData())
     {

trunk/www/admin/extensions/details.js

@@ -59 +59 @@
     var url = 'index.jsp?ID='+App.getSessionId();
     url += '&cmd=ManualScan';
-    Dialogs.openPopup(url, 'ManualScan', 900, 600);
+    Dialogs.openPopup(url, 'ManualScan', 1050, 700);
   }
   

trunk/www/admin/extensions/wizard.jsp

@@ -47 +47 @@
   import="net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter"
   import="java.util.List"
+  import="java.util.Comparator"
+  import="java.util.Collections"
   import="java.util.Date"
   import="java.io.File"
@@ -67 +69 @@
   ec.scanForChanges();
   List<ExtensionsFile> xtFiles = ec.getFiles();
+  
+  // Re-order extensions
+  Collections.sort(xtFiles, 
+    new Comparator<ExtensionsFile>()
+    {
+      public int compare(ExtensionsFile f1, ExtensionsFile f2)
+      {
+        // Sort new or modified extensions first...
+        boolean p1 = f1.isNew() || f1.wasModified();
+        boolean p2 = f2.isNew() || f2.wasModified();
+        if (p1 != p2) return p1 ? -1 : 1;
+        
+        // ...then deleted and invalid extensions...
+        p1 = f1.hasError() || !f1.exists() || !f1.isValid();
+        p2 = f2.hasError() || !f2.exists() || !f2.isValid();
+        if (p1 != p2) return p1 ? -1 : 1;
+        
+        // ...and finally all other extensions
+        return f1.getName().compareTo(f2.getName());
+      }
+    });
+  
   List<File> ignoredFiles = ec.getIgnoredFiles();
   %>
@@ -85 +109 @@
     .ignored-file td
     {
-      opacity: 0.5;
-    }
-    .ignored-file .input
-    {
-      opacity: 1;
+      color: #666666;
     }
   </style>
@@ -262 +282 @@
           <td class="cell"></td>
         </tr>
+        <tbody class="rows">
         <%
         for (File ignoredFile : ignoredFiles)
@@ -281 +302 @@
           }
           %>
-          <tbl:row clazz="ignored-file">
+          <tbl:row subclass="ignored-file">
             <tbl:cell column="file" style="white-space: nowrap;"><%=name%></tbl:cell>
             <tbl:cell column="status" style="text-align: center;">Ignored</tbl:cell>
-            <tbl:cell clazz="cell input" column="install" style="text-align: center;">
+            <tbl:cell  column="install" style="text-align: center;">
               <%
               if (allowInstall)
@@ -295 +316 @@
               %>
             </tbl:cell>
-            <tbl:cell clazz="cell input" column="ignore" style="text-align: center;">
+            <tbl:cell subclass="cell input" column="ignore" style="text-align: center;">
               <input type="checkbox" class="auto-init" data-auto-init="stop-ignore"
                 name="<%=name%>.stopignore" value="1" <%=checkStopIgnore ? "checked" : "" %>>
@@ -303 +324 @@
           <%
         }
+        %>
+        </tbody>
+        <%
       }
       %>