Changeset 7786

Timestamp:

Mar 2, 2020, 9:10:33 AM (21 months ago)

Author:

Nicklas Nordborg

Message:

Merged patch release 3.15.3 to the trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• src/clients/web/net/sf/basedb/clients/web/extensions/list/ListColumnAction.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/menu/MenuItemAction.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/section/SectionAction.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/tabcontrol/TabAction.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/ButtonAction.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/ParameterType.java (modified) (1 diff)
• src/core/net/sf/basedb/util/timer/ThreadTimerTask.java (modified) (2 diffs)
• www/common/plugin/configure.jsp (modified) (3 diffs)
• www/my_base/messages/index.jsp (modified) (1 diff)
• www/my_base/messages/list_messages.jsp (modified) (2 diffs)
• www/views/derivedbioassays/view_bioassay.jsp (modified) (1 diff)

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/list/ListColumnAction.java

@@ -22 +22 @@
 package net.sf.basedb.clients.web.extensions.list;
 
-import net.sf.basedb.clients.web.extensions.UnsafeScriptable;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Type;
@@ -42 +41 @@
   @base.modified $Date$
 */
-@UnsafeScriptable
 public interface ListColumnAction<I, V>
   extends Action

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/menu/MenuItemAction.java

@@ -22 +22 @@
 package net.sf.basedb.clients.web.extensions.menu;
 
-import net.sf.basedb.clients.web.extensions.UnsafeScriptable;
 import net.sf.basedb.util.extensions.Action;
 
@@ -45 +44 @@
   @base.modified $Date$
 */
-@UnsafeScriptable
 public interface MenuItemAction
   extends Action

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/section/SectionAction.java

@@ -22 +22 @@
 package net.sf.basedb.clients.web.extensions.section;
 
-import net.sf.basedb.clients.web.extensions.UnsafeScriptable;
 import net.sf.basedb.util.extensions.Action;
 
@@ -32 +31 @@
   @base.modified $Date$
 */
-@UnsafeScriptable
 public interface SectionAction
   extends Action

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/tabcontrol/TabAction.java

@@ -22 +22 @@
 package net.sf.basedb.clients.web.extensions.tabcontrol;
 
-import net.sf.basedb.clients.web.extensions.UnsafeScriptable;
 import net.sf.basedb.core.Help;
 import net.sf.basedb.util.extensions.Action;
@@ -33 +32 @@
   @base.modified $Date$
 */
-@UnsafeScriptable
 public interface TabAction
   extends Action

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/toolbar/ButtonAction.java

@@ -22 +22 @@
 package net.sf.basedb.clients.web.extensions.toolbar;
 
-import net.sf.basedb.clients.web.extensions.UnsafeScriptable;
 import net.sf.basedb.util.extensions.Action;
 
@@ -32 +31 @@
   @base.modified $Date:2008-03-20 12:15:25 +0100 (Thu, 20 Mar 2008) $
  */
-@UnsafeScriptable
 public interface ButtonAction
   extends Action

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

@@ -326 +326 @@
   public boolean isEnumeration()
   {
-    return (enumeration != null && enumeration.size() > 0) || (items != null && items.size() > 0);
+    return (enumeration != null) || (items != null);
   }
     

trunk/src/core/net/sf/basedb/util/timer/ThreadTimerTask.java

@@ -43 +43 @@
 {
 
+  private static final org.slf4j.Logger log = 
+    org.slf4j.LoggerFactory.getLogger(ThreadTimerTask.class);
+
   private final TimerTask task;
   private final boolean allowMultiple;
@@ -69 +72 @@
   public final synchronized void run()
   {
-    Thread t = null;
-    if (allowMultiple) 
+    try
     {
-      // We just create another thread
-      t = new Thread(task);
-    }
-    else if (!isExecuting)
-    {
-      // Create a new thread that also manages the isExecuting flag
-      isExecuting = true;
-      t = new Thread(
-        new Runnable()
-        {
-          @Override
-          public void run()
+      Thread t = null;
+      if (allowMultiple) 
+      {
+        // We just create another thread
+        t = new Thread(task);
+      }
+      else if (!isExecuting)
+      {
+        // Create a new thread that also manages the isExecuting flag
+        isExecuting = true;
+        t = new Thread(
+          new Runnable()
           {
-            try
+            @Override
+            public void run()
             {
-              task.run();
-            }
-            finally
-            {
-              isExecuting = false;
+              try
+              {
+                task.run();
+              }
+              finally
+              {
+                isExecuting = false;
+              }
             }
           }
-        }
-      );
+        );
+      }
+      else
+      {
+        // Do not allow multiple thread to execute the task
+      }
+      // Start the thread
+      if (t != null) t.start();
     }
-    else
+    catch (Throwable t)
     {
-      // Do not allow multiple thread to execute the task
+      log.error("Failed to start task: " + task, t);
     }
-    // Start the thread
-    if (t != null) t.start();
   }
   @Override

trunk/www/common/plugin/configure.jsp

@@ -80 +80 @@
 <%!
 List<?> getParameterValues(PluginParameter<?> pp, DbControl dc, javax.servlet.http.HttpServletRequest request, 
-  PluginConfigurationRequest pcRequest, ItemContext currentContext)
+  PluginConfigurationRequest pcRequest, ItemContext currentContext, Job job)
 {
   ParameterType<?> pType = pp.getParameterType();
@@ -106 +106 @@
     Object charset = currentContext.getObject("last-file-charset");
     if (charset != null) values = Collections.singletonList(charset);
+  }
+  
+  // Special handling for "dryRun" parameter which is typically not stored as a job proerty
+  if ((values == null || values.size() == 0) && Parameters.DRY_RUN_PARAMETER.equals(pp.getName()))
+  {
+    if (job != null && job.isDryRun())
+    {
+      values = Collections.singletonList(true);
+    }
   }
   
@@ -272 +281 @@
         json.put("enumeration", pType.isEnumeration() ? 1 : 0);
         json.put("multiplicity", pType.getMultiplicity());
-        List<?> values = getParameterValues(pp, dc, request, pcRequest, currentContext);
+        List<?> values = getParameterValues(pp, dc, request, pcRequest, currentContext, job);
         json.put("values", convertToJson(values, dc, pType, dateFormatter, dateTimeFormatter));
       }

trunk/www/my_base/messages/index.jsp

@@ -60 +60 @@
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 <%!
-  private static final ItemContext defaultContext = Base.createDefaultContext("timeSent", "all");
+  private static final ItemContext defaultContext = Base.createDefaultContext("timeSent", "name,from,timeSent,read,description");
   private static final Item itemType = Item.MESSAGE;
 %>

trunk/www/my_base/messages/list_messages.jsp

@@ -168 +168 @@
         exportable="true"
         formatter="<%=dateTimeFormatter%>"
+      />
+      <tbl:columndef 
+        id="read"
+        property="read"
+        datatype="boolean"
+        title="Has been read"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
       />
       <tbl:columndef 
@@ -391 +400 @@
                 <tbl:cell column="from"><%=HTML.encodeTags(item.getFrom())%></tbl:cell>
                 <tbl:cell column="timeSent" value="<%=item.getTimeSent()%>" />
+                <tbl:cell column="read" value="<%=item.isRead()%>" />
                 <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
                 <tbl:cell column="job"><base:propertyvalue item="<%=item%>" property="job" enableEditLink="<%=editLink%>" enablePropertyLink="<%=mode.hasPropertyLink()%>"/></tbl:cell>

trunk/www/views/derivedbioassays/view_bioassay.jsp

@@ -713 +713 @@
                 <tbl:row>
                   <tbl:cell column="name"><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
-                  <tbl:cell column="platform"><base:propertyvalue item="<%=item%>" property="platform" /></tbl:cell>
+                  <tbl:cell column="platform">
+                    <base:propertyvalue item="<%=item%>" property="platform" /> /
+                    <%=item.getRawDataType().toString() %>
+                  </tbl:cell>
                   <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
                 </tbl:row>