Changeset 5136

Timestamp:

Oct 15, 2009, 8:33:07 AM (12 years ago)

Author:

Nicklas Nordborg

Message:

Merged patch release 2.13.1 to the trunk.

Location:

trunk

Files:

• doc/src/docbook/admindoc/installation_upgrade.xml (modified) (4 diffs)
• src/clients/web/net/sf/basedb/clients/web/formatter/FormatterFactory.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/ArrayDesign.java (modified) (1 diff)
• src/core/net/sf/basedb/core/HibernateUtil.java (modified) (1 diff)
• src/core/net/sf/basedb/core/ItemContext.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/validator/PlatformValidator.java (modified) (3 diffs)
• www/common/share/submit_share.jsp (modified) (1 diff)
• www/filemanager/files/ajax.jsp (modified) (4 diffs)
• www/filemanager/files/edit_file_data.jsp (modified) (2 diffs)
• www/lims/arrayslides/create_wizard.jsp (modified) (1 diff)
• www/lims/arrayslides/index.jsp (modified) (2 diffs)

trunk/doc/src/docbook/admindoc/installation_upgrade.xml

@@ -7 +7 @@
 
   Copyright (C) 2007 Jari Häkkinen, Peter Johansson, Nicklas Nordborg, Martin Svensson
+  Copyright (C) 2008 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
+  Copyright (C) 2009 Jari Häkkinen, Nicklas Nordborg
 
   This file is part of BASE - BioArray Software Environment.
@@ -670 +672 @@
         <listitem>
           <para>
-            Download and install Apache Tomcat 6.0.14 or later, available
+            Download and install Apache Tomcat 6.0.20 or later, available
             from <ulink
             url="http://tomcat.apache.org" />.
@@ -1338 +1340 @@
           <listitem>
             <para>
-            The title of the message. It should be a short and consice to
+            The title of the message. It should be a short and concise to
             avoid confusion. The title will be displayed on a lot of places
             and a user may have to click on it to read the more detailed
@@ -1349 +1351 @@
           <listitem>
             <para>
-            Mark this checkbox to try to prevent new users from logging in. To
+            Mark this check-box to try to prevent new users from logging in. To
             avoid problems that can be caused by blocking the server admin out,
             the login is not completely, disabled. Any user can still login but

trunk/src/clients/web/net/sf/basedb/clients/web/formatter/FormatterFactory.java

@@ -26 +26 @@
 import net.sf.basedb.clients.web.Base;
 import net.sf.basedb.core.Annotation;
-import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.Coloring;
 import net.sf.basedb.core.ExtendedProperty;
@@ -330 +329 @@
   public static Formatter<?> getAnnotationFormatter(SessionControl sc, Annotation a, Unit unit)
   {
-    AnnotationType at = a.getAnnotationType();
     Formatter<?> f = getTypeFormatter(sc, a.getValueType());
     return a.getUnitFormatter(f, unit);

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

@@ -131 +131 @@
     ad.setNumArrays(1);
     ad.getData().setFeatureIdentificationMethod(FeatureIdentificationMethod.NONE.getValue());
+    ad.getData().setEntryDate(new Date());
     return ad;
   }

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

@@ -1236 +1236 @@
     most useful with <code>lockMode</code> = {@link LockMode#NONE} if
     the logged in user only has read permission to the object.
-    @see DbControl#reattachItem(BasicItem)
+    @see DbControl#reattachItem(BasicItem, boolean)
   */
   static void lockData(Session session, BasicData data, LockMode lockMode)

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

@@ -1293 +1293 @@
     <li>%: The rest of the string is the channel number. We use the 
       {@link Dynamic#column(VirtualColumn)} to create the expression
-      for {@link VirtualColumn#channel(int)}
+      for {@link VirtualColumn#channelRaw(int)}
 
     <li>$: The rest of the string is a raw data property name. We use

trunk/src/core/net/sf/basedb/util/overview/validator/PlatformValidator.java

@@ -24 +24 @@
 import net.sf.basedb.core.BasicItem;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.FileStoreEnabled;
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.Platform;
@@ -71 +72 @@
     BasicItem defaultVariant = OverviewUtil.getProjectDefaultItem(dc, project, Project.Default.PLATFORM_VARIANT);
     Platform platform = (Platform)node.getItem();
-    Node variantNode = node.getChild("variant");
-    PlatformVariant variant = variantNode == null ? null : (PlatformVariant)node.getItem();
+    PlatformVariant variant = null;
+    boolean failedVariant = false;
     BasicItem parentItem = parentNode.getItem();
+    try
+    {
+      variant = ((FileStoreEnabled)parentItem).getVariant();
+    }
+    catch (Throwable t)
+    {
+      // Failure to load the variant is detected by other validators
+      failedVariant = true;
+    }
     String parentTypeName = parentNode.getItemType().toString().toLowerCase();
     boolean canChangePlatform = false;
@@ -83 +93 @@
     
     if ((defaultPlatform != null && !defaultPlatform.equals(platform)) ||
-      (defaultVariant != null && !defaultVariant.equals(variant)))
+      (defaultVariant != null && !defaultVariant.equals(variant) && !failedVariant))
     {
       context.createFailure(Validator.NONDEFAULT_PLATFORM, parentNode, null,

trunk/www/common/share/submit_share.jsp

@@ -107 +107 @@
     }
     mp.updateKeys(dc, recursive);
+    sc.reloadPermissions();
     dc.commit();
     cc.removeObject("MultiPermissions");

trunk/www/filemanager/files/ajax.jsp

@@ -27 +27 @@
   import="net.sf.basedb.core.Config"
   import="net.sf.basedb.core.File"
+  import="net.sf.basedb.core.InvalidDataException"
   import="net.sf.basedb.util.Values"
   import="net.sf.basedb.util.FileUtil"
@@ -57 +58 @@
     try
     {
+      int size = Values.getInt(request.getParameter("size"), -1);
       dc = sc.newDbControl();
       File f = File.getById(dc, itemId);
@@ -68 +70 @@
       Writer toFile = new OutputStreamWriter(
           f.getUploadStream(false, f.isCompressed()), charset);
-      FileUtil.copy(in, toFile);
+      int copied = (int)FileUtil.copy(in, toFile);
+      if (size >= 0 && copied != size)
+      {
+        throw new InvalidDataException("Incomplete file; expected " + size + 
+          " bytes; got " + copied + ".");
+      }
       toFile.flush();
       toFile.close();
@@ -76 +83 @@
     catch (Exception ex)
     {
-      out.println("Failed: " + ex.getMessage());
+      out.println("Save failed: " + ex.getMessage());
       ex.printStackTrace();
     }

trunk/www/filemanager/files/edit_file_data.jsp

@@ -127 +127 @@
       var frm = document.forms['file'];
       var url = 'ajax.jsp?ID=<%=ID%>&cmd=StoreFile&item_id=<%=itemId%>';
+      url += '&size='+frm.filedata.value.length;
       var request = Main.getAjaxRequest();
       request.closeIfSuccess = closeIfSuccess;
@@ -136 +137 @@
     {
       var response = request.responseText;
-      var failed = response.indexOf('Failed') == 0;
+      var failed = response.indexOf('Save failed') == 0;
       if (!failed) 
       {

trunk/www/lims/arrayslides/create_wizard.jsp

@@ -315 +315 @@
       <input type="hidden" name="arraybatch_id" value="<%=arrayBatchId%>">
       <input type="hidden" name="quantity" value="<%=quantity%>">
-      
+      <input type="hidden" name="start_at" value="<%=startAt%>">
+            
       <h3 class="docked"><%=title%> <base:help tabcontrol="settings" /></h3>
       <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*370)+"px;"%>" 

trunk/www/lims/arrayslides/index.jsp

@@ -183 +183 @@
     dc = sc.newDbControl();
     int quantity = Values.getInt(request.getParameter("quantity"));
-    int batchId = Values.getInt(request.getParameter("arraybatch_id"));   
+    int batchId = Values.getInt(request.getParameter("arraybatch_id"));
+    int startAt = Values.getInt(request.getParameter("start_at"), 1);
     String description = Values.getStringOrNull(request.getParameter("description"));
     ArrayBatch batch = ArrayBatch.getById(dc, batchId);
@@ -195 +196 @@
       dc.saveItem(slide);
       slide.setName(Values.getStringOrNull(request.getParameter("name"+i)));
-      slide.setBatchIndex(batchId);
+      slide.setBatchIndex(startAt + i);
       
       String newBarcode = Values.getStringOrNull(request.getParameter("barcode" + i));