Changeset 5474

Timestamp:

Nov 3, 2010, 9:07:50 AM (12 years ago)

Author:

Nicklas Nordborg

Message:

Merged pre-2.16-releases to the trunk.

Location:

trunk

Files:

• doc/test/roles/index.html (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/resources/common.properties (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/resources/menu.properties (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/PresetSelector.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/table/Table.java (modified) (1 diff)
• www/biomaterials/bioplates/wells/list_biowells.jsp (modified) (8 diffs)
• www/biomaterials/extracts/edit_extract.jsp (modified) (1 diff)
• www/biomaterials/labeledextracts/edit_labeledextract.jsp (modified) (1 diff)
• www/biomaterials/samples/edit_sample.jsp (modified) (1 diff)
• www/include/menu.jsp (modified) (4 diffs)
• www/my_base/index.jsp (modified) (2 diffs)
• www/my_base/projects/set_active.jsp (modified) (2 diffs)

trunk/doc/test/roles/index.html

@@ -613 +613 @@
       <th>Name</th>
       <th>Biomaterial type</th>
-      <th>Locked wells</th>
+      <th>Well lock mode</th>
     </tr>
     <tr>
       <td>Bioplate type A</td>
-      <td>all</td>
-      <td>no</td>
+      <td>Any</td>
+      <td>Unlocked</td>
     </tr>
     </table>

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

@@ -502 +502 @@
       
       // Record this in the list of recently view items
-      if (itemId != null)
+      if (itemId != null && Nameable.class.isAssignableFrom(itemType.getItemClass()))
       {
         String recent = sc.getUserClientSetting("menu.mostRecent.viewed");

trunk/src/clients/web/net/sf/basedb/clients/web/resources/common.properties

@@ -108 +108 @@
 item.bioplate Bioplate
 item.bioplate+  Bioplates
+item.biowell  Biowell
+item.biowell+ Biowells
 item.bioplatetype Bioplate type
 item.bioplatetype+  Bioplate types
@@ -120 +122 @@
 item.plate  Plate
 item.plate+ Plates
+item.well Well
+item.well+  Wells
 item.platemapping Plate mapping
 item.platemapping+  Plate mappings
 item.arraydesign  Array design
 item.arraydesign+ Array designs
+item.feature  Feature
+item.feature+ Features
 item.arraybatch Array batch
 item.arraybatch+  Array batches
@@ -144 +150 @@
 item.client Client
 item.client+  Clients
+item.help Help
+item.help+  Help
 item.news News
 item.news+  News

trunk/src/clients/web/net/sf/basedb/clients/web/resources/menu.properties

@@ -47 +47 @@
 menu.projects.tooltip.1 Switch active project
 menu.projects.tooltip.0 Set active project
+recentprojects.title Recently used projects
 noactiveproject.title no active project
 noactiveproject.tooltip.1 No project is active

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/PresetSelector.java

@@ -260 +260 @@
     sb.append("<option value=\"\">------------------\n");
     sb.append("<option value=\"option:columns:all\" title=\"Show all columns\">All columns\n");
-    sb.append("<option value=\"option:columns:\" title=\"Show only required columns\">Required columns\n");
+    sb.append("<option value=\"option:columns:-\" title=\"Show only required columns\">Required columns\n");
     String defaultColumns = (String)cc.getObject("defaultColumns");
     if (defaultColumns != null)

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Table.java

@@ -554 +554 @@
       allVisible = false;
       visibleColumns = new LinkedHashSet<String>( Arrays.asList(columns.split(",") ));
+      visibleColumns.remove("-"); // "-" represents the required columns
     }
 

trunk/www/biomaterials/bioplates/wells/list_biowells.jsp

@@ -34 +34 @@
   import="net.sf.basedb.core.BioWell"
   import="net.sf.basedb.core.MeasuredBioMaterial"
+  import="net.sf.basedb.core.BioMaterialEvent"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.ItemResultIterator"
@@ -112 +113 @@
   {
     final ItemQuery<BioWell> query = Base.getConfiguredQuery(dc, cc, true, bioplate.getBioWells(), mode);
-    query.join(Hql.leftJoin(null, "bioMaterial", "mbm", null, false));
+    query.join(Hql.leftJoin(null, "bioMaterial", "mbm", null, true));
+    query.join(Hql.leftJoin("mbm", "creationEvent", "evt", null, true));
     if (!"row".equals(cc.getSortProperty())) query.order(Orders.asc(Hql.property("row")));
     if (!"column".equals(cc.getSortProperty())) query.order(Orders.asc(Hql.property("column")));
@@ -260 +262 @@
       <tbl:columndef 
         id="bioMaterial.name"
-        property="bioMaterial.name"
+        property="$mbm.name"
         datatype="string"
         title="[Biomtrl] Name"
@@ -269 +271 @@
       <tbl:columndef 
         id="bioMaterial.description"
-        property="bioMaterial.description"
+        property="$mbm.description"
         datatype="string"
         title="[Biomtrl] Description" 
@@ -278 +280 @@
       <tbl:columndef 
         id="bioMaterial.entryDate"
-        property="bioMaterial.entryDate"
+        property="$evt.entryDate"
         datatype="date"
         title="[Biomtrl] Registered"
@@ -391 +393 @@
               index++;
               numListed++;
+              MeasuredBioMaterial bioMaterial = null;
+              BioMaterialEvent creationEvent = null;
+              boolean editWellPermission = true;
+              try
+              {
+                bioMaterial = item.getBioMaterial();
+                if (bioMaterial != null)
+                {
+                  creationEvent = bioMaterial.getCreationEvent();
+                  editWellPermission = bioMaterial.hasPermission(Permission.WRITE) && !bioMaterial.isLockedInWell();
+                }
+                else
+                {
+                  editWellPermission = item.canAddBioMaterial();
+                }
+              }
+              catch (PermissionDeniedException ex)
+              {
+                editWellPermission = false;
+              }
               %>
               <tbl:row>
@@ -439 +461 @@
                 </tbl:cell>
                 <tbl:cell column="column" value="<%=item.getColumn()%>" />
-                <tbl:cell column="bioMaterial.name">                  
-                <%
-                MeasuredBioMaterial bioMaterial = null;
-                boolean editWellPermission = true;
-                try
-                {
-                  bioMaterial = item.getBioMaterial();
-                  if (bioMaterial != null)
-                  {
-                    editWellPermission = bioMaterial.hasPermission(Permission.WRITE) && !bioMaterial.isLockedInWell();
-                  }
-                  else
-                  {
-                    editWellPermission = item.canAddBioMaterial();
-                  }
-                }
-                catch (PermissionDeniedException ex)
-                {
-                  editWellPermission = false;
-                }
-                %>
+                <tbl:cell column="bioMaterial.name">
                   <base:propertyvalue 
                       item="<%=item%>" 
@@ -478 +480 @@
                   />
                 </tbl:cell>
+                <tbl:cell column="bioMaterial.description"><base:propertyvalue item="<%=item%>" property="bioMaterial.description"/></tbl:cell>
+                <tbl:cell column="bioMaterial.entryDate" value="<%=creationEvent == null ? null : creationEvent.getEntryDate() %>" />
                 <tbl:cell column="originalBioMaterial.name"><base:propertyvalue item="<%=item%>" property="originalBioMaterial" /></tbl:cell>
                 <tbl:cell column="permission"><%=PermissionUtil.getShortPermissions(item)%></tbl:cell>

trunk/www/biomaterials/extracts/edit_extract.jsp

@@ -398 +398 @@
       }
       url += '&bioplate_id='+bioplateId;
-      url += '&resetTemporary=1&tmpfilter:STRING:bioMaterial.name='+escape('=');
+      url += '&resetTemporary=1&tmpfilter:STRING:$mbm.name='+escape('=');
       url += '&tmpfilter:STRING:originalBioMaterial.name='+escape('=');
       url += '&columns=row,column';

trunk/www/biomaterials/labeledextracts/edit_labeledextract.jsp

@@ -429 +429 @@
       }
       url += '&bioplate_id='+bioplateId;
-      url += '&resetTemporary=1&tmpfilter:STRING:bioMaterial.name='+escape('=');
+      url += '&resetTemporary=1&tmpfilter:STRING:$mbm.name='+escape('=');
       url += '&tmpfilter:STRING:originalBioMaterial.name='+escape('=');
       url += '&columns=row,column';

trunk/www/biomaterials/samples/edit_sample.jsp

@@ -400 +400 @@
       }
       url += '&bioplate_id='+bioplateId;
-      url += '&resetTemporary=1&tmpfilter:STRING:bioMaterial.name='+escape('=');
+      url += '&resetTemporary=1&tmpfilter:STRING:$mbm.name='+escape('=');
       url += '&tmpfilter:STRING:originalBioMaterial.name='+escape('=');
       url += '&columns=row,column';

trunk/www/include/menu.jsp

@@ -51 +51 @@
   import="net.sf.basedb.core.Include"
   import="net.sf.basedb.core.ItemResultList"
+  import="net.sf.basedb.core.Type"
   import="net.sf.basedb.core.query.Orders"
   import="net.sf.basedb.core.query.Order"
   import="net.sf.basedb.core.query.Hql"
+  import="net.sf.basedb.core.query.Restrictions"
+  import="net.sf.basedb.core.query.Expressions"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.util.HTML"
@@ -73 +76 @@
   import="java.util.Arrays"
   import="java.util.Iterator"
+  import="java.util.Set"
+  import="java.util.HashSet"
 %>
 <%@ taglib prefix="m" uri="/WEB-INF/menu.tld" %>
@@ -97 +102 @@
     style="display: none"
     >
+    <%
+    final DbControl dc = sc.newDbControl();
+    boolean menuSeparatorBeforeDeactivate = true;
+    try
+    {
+      List<Project> projects = new ArrayList<Project>();
+      int lastRecentActiveIndex = 0;
+      // 1. Load the most recently active projects
+      String tmp = sc.getUserClientSetting("projects.recentActive");
+      Set<Integer> recentProjects = new HashSet<Integer>();
+      if (tmp != null)
+      {
+        for (String id : tmp.split(":"))
+        {
+          try
+          {
+            Project p = Project.getById(dc, Values.getInt(id));
+            if (!p.isRemoved())
+            {
+              recentProjects.add(p.getId());
+              projects.add(p);
+              lastRecentActiveIndex++;
+            }
+          }
+          catch (RuntimeException ex)
+          {}
+        }
+      }
+      
+      // 2. Load more projects 
+      final ItemContext projectCC = sc.getCurrentContext(Item.PROJECT);
+      final ItemQuery<Project> projectQuery = Project.getQuery();
+      projectQuery.include(Include.MINE, Include.SHARED);
+      projectQuery.restrict(Restrictions.not(Restrictions.in(Hql.property("id"), Expressions.parameter("projects"))));
+      projectQuery.setParameter("projects", recentProjects, Type.INT);
+      Order projectSortOrder = projectCC.getSortOrder();
+      if (projectSortOrder != null) projectQuery.order(projectSortOrder);
+      projectQuery.order(Orders.asc(Hql.property("name")));
+      projectQuery.setCacheResult(true);
+      projects.addAll(projectQuery.list(dc));
+      boolean breakAt15 = projects.size() > 16;
+      int index = 0;
+      String thisIsTheActiveProject = menu.getString("activeproject.tooltip");
+      String thisIsNotTheActiveProject = menu.getString("inactiveproject.tooltip");
+      if (lastRecentActiveIndex > 0)
+      {
+        %>
+        <m:menuitem 
+          title="<%=menu.getString("recentprojects.title")%>" 
+          style="font-weight: bold; color: #000000; background: #e8e8e8;" 
+          enabled="false" 
+        />
+        <m:menuseparator />
+        <%
+      }
+      Set<Integer> shownProjects = new HashSet<Integer>();
+      for (Project p : projects)
+      {
+        if (index == 15 && breakAt15) break;
+        index++;
+        int projectId = p.getId();
+        boolean active = activeProjectId == projectId;
+        String prefix = index <= lastRecentActiveIndex ? index + ". " : "";
+        shownProjects.add(p.getId());
+        String link = active ? 
+          "Menu.openUrl('"+root+"my_base/projects/index.jsp?ID="+ID+"&cmd=ViewItem&item_id=" + projectId + "')" : 
+          "Main.openPopup('"+root+"my_base/projects/set_active.jsp?ID="+ID+"&project_id="+p.getId()+"', 'ActivateProject', 300, 140)";
+        %>
+        <m:menuitem
+          title="<%=prefix + HTML.encodeTags(p.getName())%>"
+          style="<%=active ? "color: #000000; font-weight: bold;" : null %>"
+          onclick="<%=link%>"
+          icon="<%=active ? "checkedmenu.gif" : null%>"
+          tooltip="<%=active ? thisIsTheActiveProject : thisIsNotTheActiveProject%>"
+        />
+        <%
+        if (index == lastRecentActiveIndex)
+        {
+          %>
+          <m:menuseparator />
+          <%
+          menuSeparatorBeforeDeactivate = false;
+        }
+        else
+        {
+          menuSeparatorBeforeDeactivate = true;
+        }
+      }
+      if (breakAt15)
+      {
+        int more = projects.size() - 15;
+        %>
+        <m:menuitem 
+          title="<%="…" + menu.getString("moreprojects.title", Integer.toString(more))%>"
+          onclick="<%="Menu.openUrl('"+root+"my_base/projects/index.jsp?ID="+ID+"&cmd=UpdateContext&tmpfilter:INT:id=<>"+Values.getString(shownProjects, "|", true)+"')"%>"
+          tooltip="<%=menu.getString("moreprojects.tooltip")%>"
+        />
+        <%
+      }
+    }
+    catch (Throwable t)
+    {
+      t.printStackTrace();
+      menuSeparatorBeforeDeactivate = false;
+      %>
+      <m:menuseparator />
+      <m:menuitem 
+        title="<%=menu.getString("projects.error.title")%>" 
+        tooltip="<%=menu.getString("projects.error.tooltip", t.getMessage())%>"
+        enabled="false"
+        icon="error.gif"
+      />
+      <%
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+    if (menuSeparatorBeforeDeactivate)
+    {
+      %>
+      <m:menuseparator />
+      <%
+    }
+    %>
     <m:menuitem
       title="<%="<i>- " + menu.getString("noactiveproject.title") + " -</i>"%>"
@@ -104 +234 @@
       tooltip="<%=menu.getString("noactiveproject.tooltip", activeProjectId == 0)%>"
     />
-    <%
-    final DbControl dc = sc.newDbControl();
-    try
-    {
-      final ItemContext projectCC = sc.getCurrentContext(Item.PROJECT);
-      final ItemQuery<Project> projectQuery = Project.getQuery();
-      projectQuery.include(Include.MINE, Include.SHARED);
-      Order projectSortOrder = projectCC.getSortOrder();
-      if (projectSortOrder != null) projectQuery.order(projectSortOrder);
-      projectQuery.order(Orders.asc(Hql.property("name")));
-      projectQuery.setCacheResult(true);
-      ItemResultList<Project> projects = projectQuery.list(dc);
-      boolean breakAt20 = projects.size() > 25;
-      int index = 0;
-      String thisIsTheActiveProject = menu.getString("activeproject.tooltip");
-      String thisIsNotTheActiveProject = menu.getString("inactiveproject.tooltip");
-      for (Project p : projects)
-      {
-        if (index == 20 && breakAt20) break;
-        index++;
-        int projectId = p.getId();
-        boolean active = activeProjectId == projectId;
-        %>
-        <m:menuitem
-          title="<%=HTML.encodeTags(p.getName())%>"
-          style="<%=active ? "color: #000000; font-weight: bold;" : null %>"
-          onclick="<%="Main.openPopup('"+root+"my_base/projects/set_active.jsp?ID="+ID+"&project_id="+p.getId()+"', 'ActivateProject', 300, 140)"%>"
-          icon="<%=active ? "checkedmenu.gif" : null%>"
-          enabled="<%=!active%>"
-          tooltip="<%=active ? thisIsTheActiveProject : thisIsNotTheActiveProject%>"
-        />
-        <%
-      }
-      if (breakAt20)
-      {
-        int more = projects.size() - 20;
-        %>
-        <m:menuseparator />
-        <m:menuitem 
-          title="<%=menu.getString("moreprojects.title", Integer.toString(more))%>"
-          onclick="<%="Menu.openUrl('"+root+"my_base/projects/index.jsp?ID="+ID+"')"%>"
-          tooltip="<%=menu.getString("moreprojects.tooltip")%>"
-        />
-        <%
-      }
-    }
-    catch (Throwable t)
-    {
-      t.printStackTrace();
-      %>
-      <m:menuseparator />
-      <m:menuitem 
-        title="<%=menu.getString("projects.error.title")%>" 
-        tooltip="<%=menu.getString("projects.error.tooltip", t.getMessage())%>"
-        enabled="false"
-        icon="error.gif"
-      />
-      <%
-    }
-    finally
-    {
-      if (dc != null) dc.close();
-    }
-    %>
   </m:menu>
   <%

trunk/www/my_base/index.jsp

@@ -55 +55 @@
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
   import="net.sf.basedb.util.Values"
-  import="java.util.Date"
+  import="java.util.Date" 
+  import="java.util.List"
+  import="java.util.ArrayList"
+  import="java.util.Set"
+  import="java.util.HashSet"
 %>
 <%@ taglib
@@ -108 +112 @@
   ItemResultList<Message> messages = messageQuery.list(dc);
   
+  List<Project> projects = new ArrayList<Project>();
+  String tmp = sc.getUserClientSetting("projects.recentActive");
+  Set<Integer> recentProjects = new HashSet<Integer>();
+  if (tmp != null)
+  {
+    for (String id : tmp.split(":"))
+    {
+      try
+      {
+        Project p = Project.getById(dc, Values.getInt(id));
+        if (!p.isRemoved())
+        {
+          recentProjects.add(p.getId());
+          projects.add(p);
+        }
+      }
+      catch (RuntimeException ex)
+      {}
+    }
+  }
   ItemQuery<Project> projectQuery = Project.getQuery();
   projectQuery.order(Orders.asc(Hql.property("name")));
   projectQuery.include(Include.MINE, Include.SHARED);
-  ItemResultList<Project> projects = projectQuery.list(dc);
+  projectQuery.restrict(Restrictions.not(Restrictions.in(Hql.property("id"), Expressions.parameter("projects"))));
+  projectQuery.setParameter("projects", recentProjects, Type.INT);
+  projects.addAll(projectQuery.list(dc));
   
   QuotaType totalQuotaType = QuotaType.getById(dc, SystemItems.getId(QuotaType.TOTAL));

trunk/www/my_base/projects/set_active.jsp

@@ -32 +32 @@
   import="net.sf.basedb.core.Include"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.StringUtil"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.util.Values"
   import="net.sf.basedb.clients.web.util.HTML"
+  import="java.util.List"
+  import="java.util.ArrayList"
+  import="java.util.Arrays"
 %>
 <%@ taglib
@@ -60 +64 @@
   sc.setActiveProject(p);
   sc.setUserClientSetting("projects.lastactive", projectId == 0 ? null : Integer.toString(projectId));
+  if (projectId != 0)
+  {
+    String recent = sc.getUserClientSetting("projects.recentActive");
+    List<String> recentActive = null;
+    if (recent == null)
+    {
+      recentActive = new ArrayList<String>();
+    }
+    else
+    {
+      // Need a new list since Arrays.asList returns a read-only list
+      recentActive = new ArrayList<String>(Arrays.asList(recent.split(":")));
+    }
+    String thisProject = Integer.toString(projectId);
+    recentActive.remove(thisProject);
+    recentActive.add(0, thisProject);
+    int maxRecent = Values.getInt(sc.getUserClientSetting("menu.mostRecent.maxViewed"), 6);
+    if (recentActive.size() > maxRecent) recentActive = recentActive.subList(0, maxRecent);
+    sc.setUserClientSetting("projects.recentActive", StringUtil.join(recentActive, ":", true));
+  }
   sc.setSessionSetting("menu.standard.html", null);
   if (p == null)