Changeset 5687

Timestamp:

Aug 9, 2011, 1:39:40 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1597: Subtypes of items

Smarter selection of default subtypes and related items (protocols, etc) have now been implemented in the other important edit dialogs.

Added support for also loading and displaying project default items dynamically based on the selected subtype.

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/taglib/Select.java (modified) (7 diffs)
• src/core/net/sf/basedb/core/Project.java (modified) (6 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/AbstractItemImporter.java (modified) (3 diffs)
• src/test/TestProject.java (modified) (1 diff)
• www/WEB-INF/base.tld (modified) (1 diff)
• www/admin/itemsubtypes/ajax.jsp (modified) (5 diffs)
• www/biomaterials/extracts/edit_extract.jsp (modified) (14 diffs)
• www/biomaterials/extracts/index.jsp (modified) (4 diffs)
• www/biomaterials/samples/edit_sample.jsp (modified) (5 diffs)
• www/biomaterials/samples/index.jsp (modified) (1 diff)
• www/include/scripts/subtypes.js (modified) (2 diffs)
• www/lims/arraybatches/edit_batch.jsp (modified) (5 diffs)
• www/lims/arraydesigns/edit_design.jsp (modified) (4 diffs)
• www/views/derivedbioassays/edit_bioassay.jsp (modified) (17 diffs)
• www/views/derivedbioassays/index.jsp (modified) (4 diffs)
• www/views/physicalbioassays/edit_bioassay.jsp (modified) (15 diffs)
• www/views/physicalbioassays/index.jsp (modified) (3 diffs)
• www/views/rawbioassays/edit_rawbioassay.jsp (modified) (8 diffs)

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Select.java

@@ -22 +22 @@
 package net.sf.basedb.clients.web.taglib;
 
+import java.util.Collections;
 import java.util.List;
 
@@ -315 +316 @@
   
   /**
-      The project default value
-  */
-  private transient BasicItem defaultitem;
+      The project default values.
+  */
+  private transient List<? extends BasicItem> defaultItems;
   
   /**
@@ -481 +482 @@
   public void setDefaultitem(BasicItem defaultitem)
   {
-    this.defaultitem = defaultitem;
-  }
-  public BasicItem getDefaultitem()
-  {
-    return defaultitem;
+    this.defaultItems = defaultitem == null ? null : Collections.singletonList(defaultitem);
+  }
+  
+  public void setDefaultitems(List<? extends BasicItem> defaultItems)
+  {
+    this.defaultItems = defaultItems;
   }
   
@@ -584 +586 @@
         sb.append("<option value=\"0\">").append(getUnselectedtext()).append("\n");
       }
+      boolean hasSelected = false;
       if (current != null)
       {
@@ -589 +592 @@
         sb.append(current.getId() * (isNewitem() ? 1 : -1));
         sb.append("\" selected>");
+        hasSelected = true;
         String name = getName(current);
         sb.append(HTML.encodeTags(name)).append("\n");
@@ -607 +611 @@
           sb.append("<option value=\"").append(item.getId()).append("\"");
           sb.append(" class=\"").append(clazz).append("\"");
-          if (i == 1 && current == null && isNewitem() && getSelectrecent()) 
+          if (!hasSelected && isNewitem() && getSelectrecent()) 
           {
             sb.append(" selected");
+            hasSelected = true;
           }
           sb.append(">").append(i).append(". ").append(name).append("\n");
@@ -615 +620 @@
         }
       }
-      if (defaultitem != null)
-      {
-        sb.append("<option value=\"0\" disabled=\"true\" class=\"defaultheader\">- default -\n");
-        String name = getName(defaultitem);
-        String clazz = "default";
-        
-        sb.append("<option value=\"").append(defaultitem.getId()).append("\"");
-        sb.append(" class=\"").append(clazz).append("\"");        
-        if ( current == null && 
-            (recent != null && recent.isEmpty()) && 
-            isNewitem() && 
-            getSelectdefault() )
-        {         
-          sb.append(" selected");
+      if (defaultItems != null && defaultItems.size() > 0)
+      {
+        sb.append("<option value=\"0\" disabled=\"true\" class=\"defaultheader\">- project default -\n");
+        for (BasicItem defaultitem : defaultItems)
+        {
+          String name = getName(defaultitem);
+          
+          sb.append("<option value=\"").append(defaultitem.getId()).append("\"");
+          sb.append(" class=\"default\"");        
+          if (!hasSelected && isNewitem() && getSelectdefault())
+          {         
+            sb.append(" selected");
+            hasSelected = true;
+          }
+          sb.append(">").append(name).append("\n");
         }
-        sb.append(">").append(name).append("\n");
       }
     }

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

@@ -39 +39 @@
 import net.sf.basedb.info.ProjectInfo;
 import net.sf.basedb.info.ToTransferable;
+import net.sf.basedb.util.EqualsHelper;
 
 import java.util.ArrayList;
@@ -674 +675 @@
   
   /**
-    Find a default item of the given item type. If the project contains
-    more than one default item, the first one found is selected.
+    Find the default items of the given item type. If the strict parameter
+    is true, the search will only match items without a subtype. If strict
+    is false, the search ignore the subtype.
+    
     @param dc A DbControl for database access
     @param itemType The type of item to find
-    @return The item that was found, or null
+    @return A list with the items that was found (empty if no item was found)
     @since 3.0
   */
-  public BasicItem findDefaultItem(DbControl dc, Item itemType)
+  public List<? extends BasicItem> findDefaultItems(DbControl dc, Item itemType, boolean strict)
   {
     if (itemType == null) throw new InvalidUseOfNullException("itemType");
-    BasicData defaultData = findDefaultData(itemType, null, false);
-    return dc.getItem(BasicItem.class, defaultData);
-  }
-  
-  /**
-    Find a default (subtypable) item that has the given subtype. If the
+    List<BasicData> defaultData = findAllDefaultData(itemType, null, strict);
+    List<BasicItem> defaultItems = new ArrayList<BasicItem>(defaultData.size());
+    for (BasicData data : defaultData)
+    {
+      defaultItems.add(dc.getItem(BasicItem.class, data));
+    }
+    return defaultItems;
+  }
+  
+  /**
+    Find the default (subtypable) items that has the given subtype. If the
     strict parameter is true, an exact match must be found, otherwise
     the search is repeated to find an item without a subtype. The search
@@ -698 +706 @@
     @param strict TRUE to strictly match the subtype, FALSE to also
       search for items without subtype
-    @return The item that was found, or null
+    @return A list with the items that was found (empty if no item was found)
     @since 3.0
   */
-  public BasicItem findDefaultItem(DbControl dc, ItemSubtype subtype, boolean strict)
+  public List<? extends BasicItem> findDefaultItems(DbControl dc, ItemSubtype subtype, boolean strict)
   {
     if (subtype == null) throw new InvalidUseOfNullException("subtype");
-    BasicData defaultData = findDefaultData(subtype.getMainItemType(), subtype.getData(), strict);
-    return dc.getItem(BasicItem.class, defaultData);
+    List<BasicData> defaultData = findAllDefaultData(subtype.getMainItemType(), subtype.getData(), strict);
+    List<BasicItem> defaultItems = new ArrayList<BasicItem>(defaultData.size());
+    for (BasicData data : defaultData)
+    {
+      defaultItems.add(dc.getItem(BasicItem.class, data));
+    }
+    return defaultItems;
+  }
+  
+  /**
+    Utility method for finding default items of the given relatedType.
+    If a subtype is given this method first try to find the related
+    subtype for the given relatedType. If no subtype is given or if no
+    related subtype is found, this method behaves as if {@link #findDefaultItems(DbControl, Item, boolean)}
+    was called with strict=true (eg. it will only find items that doesn't have a subtype).
+    If a related subtype is found this method behaves as if 
+    {@link #findDefaultItems(DbControl, ItemSubtype, boolean)}
+    was called with the related subtype and strict=false.
+    
+    @param dc A DbControl for database access
+    @param subtype The main subtype
+    @param relatedType The related item type that we are interested in
+    @return A list with the items that was found (empty if no item was found)
+    @since 3.0
+  */
+  public List<? extends BasicItem> findDefaultItemsOfRelatedSubtype(DbControl dc, ItemSubtype subtype, Item relatedType)
+  {
+    ItemSubtype related = subtype == null ? null : subtype.getRelatedSubtype(relatedType);
+    if (related == null)
+    {
+      return findDefaultItems(dc, relatedType, true);
+    }
+    else
+    {
+      return findDefaultItems(dc, related, false);
+    }
   }
   
@@ -788 +830 @@
   /**
     Find a default item in this project of the given item type (required)
-    and subtype (optional). If a subtype is given, this method first try to
-    match exactly. If no item is found, and strict is false, a second attempt
-    is made to match against items WITHOUT subtype (items with a different
-    subtype are never matched). If more than one item matches the critera, 
-    the first one found is returned. 
+    and subtype (optional). This method will first try to locate an
+    exact match for the given item type and subtype. If no items are found
+    and strict is false, a second attempt is made to match items as follows:
+    If a subtype is given it will match items WITHOUT a subtype (items with
+    a different subtype are not matched). If no subtype is given, the search
+    ignore the subtype on the other items.
+    
+    <p>
+    If more than one item matches the critera, the first one found is returned. 
     
       @param itemType The main item type of the item we are looking for
@@ -811 +857 @@
       if (dataClass.isInstance(data))
       {
-        // If no subtype is given we have found a match
-        if (subtype == null) 
+        // Found an item of the correct item type... get it's subtype
+        ItemSubtypeData otherSubtype = null;
+        if (data instanceof SubtypableData)
+        {
+          otherSubtype = ((SubtypableData)data).getItemSubtype();
+        }
+        
+        // If the subtypes are null or equal we have found a match
+        if (EqualsHelper.equals(subtype, otherSubtype)) 
         {
           bestMatch = data;
@@ -818 +871 @@
         }
         
-        // Check the subtype
-        if (data instanceof SubtypableData)
-        {
-          ItemSubtypeData otherSubtype = ((SubtypableData)data).getItemSubtype();
-          if (subtype.equals(otherSubtype))
-          {
-            // Found an exact match
-            bestMatch = data;
-            break;
-          }
-          
-          // This is a possible (non-strict) match -- do not update if already set
-          if (!strict && otherSubtype == null && bestMatch == null)
+        if (!strict && bestMatch == null)
+        {
+          // Is this maybe the first non-strict match?
+          if (subtype == null || otherSubtype == null)
           {
             bestMatch = data;
           }
         }
-        
       }
     } 
     return bestMatch;
+  }
+
+  /**
+    Find all default items in this project of the given item type (required)
+    and subtype (optional). If a subtype is given, this method first try to
+    match exactly. If no item is found, and strict is false, a second attempt
+    is made to match against items WITHOUT subtype (items with a different
+    subtype are never matched). 
+    
+      @param itemType The main item type of the item we are looking for
+      @param subtype The subtype of the item we are looking for (optional)
+      @param strict TRUE if the subtype must match
+      @since 3.0
+  */
+  List<BasicData> findAllDefaultData(Item itemType, ItemSubtypeData subtype, boolean strict)
+  {
+    ItemParameterValueData defaultItems = getData().getDefaultItems();
+    if (defaultItems == null) return null;
+    
+    List<BasicData> result = new ArrayList<BasicData>();
+    List<BasicData> nonStrictMatches = strict ? null : new ArrayList<BasicData>();
+    
+    Class dataClass = itemType.getDataClass();
+    for (BasicData data : defaultItems.getValues())
+    {
+      if (dataClass.isInstance(data))
+      {
+        // Found an item of the correct item type... get it's subtype
+        ItemSubtypeData otherSubtype = null;
+        if (data instanceof SubtypableData)
+        {
+          otherSubtype = ((SubtypableData)data).getItemSubtype();
+        }
+        
+        // If the subtypes are null or equal we have found a match
+        if (EqualsHelper.equals(subtype, otherSubtype)) 
+        {
+          result.add(data);
+        }
+        else if (!strict)
+        {
+          // Non-strict matches
+          if (subtype == null || otherSubtype == null)
+          {
+            nonStrictMatches.add(data);
+          }
+        }
+      }
+    }
+    if (result.size() == 0 && !strict) result.addAll(nonStrictMatches);
+    return result;
   }
 

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

@@ -1285 +1285 @@
   }
   /**
-    Get the default platform of the currently active project.
+    Get the default platform of the currently active project. If there
+    is more than one default platform, the first one is selected.
     @return The active platform, or null if no project is active or
       the project doesn't specify a platform
@@ -1294 +1295 @@
     if (sc.getActiveProjectId() == 0) return null;
     Project activeProject = Project.getById(dc, sc.getActiveProjectId());
-    return (Platform)activeProject.findDefaultItem(dc, Item.PLATFORM);
+    List<? extends BasicItem> platforms = activeProject.findDefaultItems(dc, Item.PLATFORM, true);
+    return platforms == null || platforms.size() == 0 ? null : (Platform)platforms.get(0);
   }
   
@@ -1307 +1309 @@
     if (sc.getActiveProjectId() == 0) return null;
     Project activeProject = Project.getById(dc, sc.getActiveProjectId());
-    return (PlatformVariant)activeProject.findDefaultItem(dc, Item.PLATFORMVARIANT);
+    List<? extends BasicItem> platforms = activeProject.findDefaultItems(dc, Item.PLATFORMVARIANT, true);
+    return platforms == null || platforms.size() == 0 ? null : (PlatformVariant)platforms.get(0);
   }
   

trunk/src/test/TestProject.java

@@ -139 +139 @@
       Project p = Project.getById(dc, project_id);
       
-      BasicItem found = null;
+      List<? extends BasicItem> found = null;
       if (subtypeId == 0)
       {
-        found = p.findDefaultItem(dc, defaultType);
+        found = p.findDefaultItems(dc, defaultType, true);
       }
       else
       {
         ItemSubtype subtype = ItemSubtype.getById(dc, subtypeId);
-        found = p.findDefaultItem(dc, subtype, true);
+        found = p.findDefaultItems(dc, subtype, true);
       }
       
-      if (found == null)
+      if (found == null || found.size() == 0)
       {
         throw new ItemNotFoundException("Default " + defaultType + " for project: " + p);
       }
-      else if (found.getId() != expectedId)
+      else if (found.get(0).getId() != expectedId)
       {
         throw new RuntimeException("Found " + found);

trunk/www/WEB-INF/base.tld

@@ -433 +433 @@
     </attribute>
     <attribute>
+      <name>defaultitems</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
       <name>selectdefault</name>
       <required>false</required>

trunk/www/admin/itemsubtypes/ajax.jsp

@@ -27 +27 @@
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.Project"
   import="net.sf.basedb.core.ItemSubtype"
   import="net.sf.basedb.core.Subtypable"
   import="net.sf.basedb.core.BasicItem"
   import="net.sf.basedb.core.Nameable"
+  import="net.sf.basedb.core.SystemItems"
+  import="net.sf.basedb.core.Protocol"
+  import="net.sf.basedb.core.Hardware"
+  import="net.sf.basedb.core.Software"
   import="net.sf.basedb.core.InvalidDataException"
   import="net.sf.basedb.util.Values"
@@ -91 +96 @@
     dc = sc.newDbControl();
 
+    // The main item's subtype
     ItemSubtype subtype = itemId == 0 ? null : ItemSubtype.getById(dc, itemId);
-    Item mainItemType = subtype == null ? Item.valueOf(request.getParameter("itemType")) : subtype.getMainItemType();
-    ItemContext cc = sc.getCurrentContext(mainItemType);
-
+    Item mainItemType = null;
     if (subtype != null)
     {
+      mainItemType = subtype.getMainItemType();
       json.put("id", subtype.getId());
       json.put("name", subtype.getName());
     }
+    else
+    {
+      mainItemType = Item.valueOf(request.getParameter("itemType"));
+    }
+
+    // Current context for the main item
+    ItemContext cc = sc.getCurrentContext(mainItemType);
+
+    // Active project
+    Project activeProject = sc.getActiveProjectId() > 0 ? Project.getById(dc, sc.getActiveProjectId()) : null;
     
+    // Related item types
     for (String relatedType : request.getParameterValues("relatedType"))
     {
@@ -107 +123 @@
       
       // Load the related subtype
+      ItemSubtype relatedSubtype = null;
       if (subtype != null)
       {
-        ItemSubtype relatedSubtype = subtype.getRelatedSubtype(relatedItem);
+        relatedSubtype = subtype.getRelatedSubtype(relatedItem);
         if (relatedSubtype != null)
         {
@@ -119 +136 @@
       }
       
+      if (relatedSubtype == null)
+      {
+        // Find a default related subtype
+        String systemId = null;
+        if (relatedItem == Item.PROTOCOL)
+        {
+          systemId = Protocol.getDefaultSystemId(mainItemType);
+        }
+        else if (relatedItem == Item.HARDWARE)
+        {
+          systemId = Hardware.getDefaultSystemId(mainItemType);
+        }
+        else if (relatedItem == Item.SOFTWARE)
+        {
+          systemId = Software.getDefaultSystemId(mainItemType);
+        }
+        if (systemId != null) 
+        {
+          relatedSubtype = ItemSubtype.getById(dc, SystemItems.getId(systemId));
+        }
+      }
+      
       // Load the most recently used items
       List<? extends BasicItem> recentItems = cc.getRecent(dc, relatedItem, subtype);
@@ -133 +172 @@
         jsonITEM.put("recent", jsonRecent);
       }
+      
+      // Load project default items
+      if (activeProject != null)
+      {
+        List<? extends BasicItem> defaultItems = relatedSubtype != null ?
+            activeProject.findDefaultItems(dc, relatedSubtype, false) : activeProject.findDefaultItems(dc, relatedItem, true);
+            
+        JSONArray jsonDefault = new JSONArray();
+        for (BasicItem defaultItem : defaultItems)
+        {
+          JSONObject jsonDefaultItem = new JSONObject();
+          jsonDefaultItem.put("id", defaultItem.getId());
+          jsonDefaultItem.put("name", ((Nameable)defaultItem).getName());
+          jsonDefault.add(jsonDefaultItem);
+        }
+        jsonITEM.put("default", jsonDefault);
+      }
+      
       json.put(relatedType, jsonITEM);
     }

trunk/www/biomaterials/extracts/edit_extract.jsp

@@ -54 +54 @@
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.Values"
+  import="net.sf.basedb.util.ListUtil"
   import="net.sf.basedb.util.formatter.Formatter"
   import="net.sf.basedb.util.formatter.WellCoordinateFormatter"
@@ -67 +68 @@
   import="java.util.HashSet"
   import="java.util.Date"
+  import="java.util.Collections"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
@@ -91 +93 @@
 
   boolean readCurrentSubtype = true;
-  int currentSubtypeId = 0;
+  ItemSubtype currentSubtype = null;
   boolean readCurrentProtocol = true;
   Protocol currentProtocol = null;
-  Protocol defaultProtocol = null;
   boolean readCurrentTag = true;
   Tag currentTag = null;
@@ -108 +109 @@
   BioPlate currentBioPlate = null;
   
-  // Load recently used items
-  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL);
-  List<Sample> recentSamples = (List<Sample>)cc.getRecent(dc, Item.SAMPLE);
-  List<BioPlate> recentBioPlates = (List<BioPlate>)cc.getRecent(dc, Item.BIOPLATE);
-  List<Tag> recentTags = (List<Tag>)cc.getRecent(dc, Item.TAG);
-
-  int activeProjectId = sc.getActiveProjectId();
-  if (activeProjectId > 0)
-  {
-    Project activeProject = Project.getById(dc, activeProjectId);
-    try
-    {
-      defaultProtocol = (Protocol)activeProject.findDefaultItem(dc, 
-          ItemSubtype.getById(dc, SystemItems.getId(Protocol.EXTRACTION)), false);
-    }
-    catch(PermissionDeniedException pdex)
-    {
-      defaultProtocol = null;
-    }
-  }
   if (itemId == 0)
   {
@@ -140 +121 @@
       currentTag = Base.getFirstMatching(dc, Tag.getQuery(), "name", cc.getPropertyFilter("tag.name"));
     }
-    currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
-    if (currentSubtypeId == 0) 
-    {
-      int recentSubtypeId = Values.getInt(cc.getRecent(Item.ITEMSUBTYPE.name(), 0));
-      currentSubtypeId = Values.getInt(cc.getPropertyValue("itemSubtype"), recentSubtypeId);
-    }
+    int currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
+    List<ItemSubtype> relatedToParent = Collections.emptyList();
     int sampleId = Values.getInt(request.getParameter("sample_id"));
     int extractId = Values.getInt(request.getParameter("extract_id"));
+
     if (sampleId != 0)
     {
@@ -153 +131 @@
       parentType = Item.SAMPLE;
       name = currentSample.getName() + ".e" + (currentSample.countExtracts() + 1);      
+      if (currentSubtypeId == 0)
+      {
+        relatedToParent = ItemSubtype.getParentSubtypes(dc, currentSample, Item.EXTRACT);
+      }
     }
     else if (extractId != 0)
@@ -161 +143 @@
       extractsQuery = Extract.getQuery();
       extractsQuery.restrict(Restrictions.eq(Hql.property("id"), Expressions.integer(extractId)));
+      if (currentSubtypeId == 0)
+      {
+        relatedToParent = ItemSubtype.getParentSubtypes(dc, e, Item.EXTRACT);
+      }
     }
     else if (Values.getBoolean(request.getParameter("pooled")))
@@ -173 +159 @@
     {
       name = Values.getString(cc.getPropertyValue("name"), "New extract");
+    }
+    if (currentSubtypeId == 0) 
+    {
+      if (relatedToParent.size() > 0)
+      {
+        // Find most recently used related subtype
+        List<ItemSubtype> recentSubtypes = (List<ItemSubtype>)cc.getRecent(dc, Item.ITEMSUBTYPE);
+        currentSubtype = ListUtil.findFirstCommon(recentSubtypes, relatedToParent, relatedToParent.get(0));
+      }
+      else
+      {
+        int recentSubtypeId = Values.getInt(cc.getRecent(Item.ITEMSUBTYPE.name(), 0));
+        currentSubtypeId = Values.getInt(cc.getPropertyValue("itemSubtype"), recentSubtypeId);
+        if (currentSubtypeId > 0) currentSubtype = ItemSubtype.getById(dc, currentSubtypeId);
+      }
     }
     eventDate = (Date)cc.getPropertyObject("creationEvent.eventDate");    
@@ -191 +192 @@
     try
     {
-      ItemSubtype subtype = extract.getItemSubtype();
-      if (subtype != null) currentSubtypeId = subtype.getId();
+      currentSubtype = extract.getItemSubtype();
     }
     catch (PermissionDeniedException ex)
@@ -253 +253 @@
     }
   }
+  
+  // Default items 
+  int activeProjectId = sc.getActiveProjectId();
+  List<Protocol> defaultProtocols = null;
+  if (activeProjectId > 0)
+  {
+    Project activeProject = Project.getById(dc, activeProjectId);
+    ItemSubtype protocolSubtype = currentSubtype == null ? null : currentSubtype.getRelatedSubtype(Item.PROTOCOL);
+    if (protocolSubtype == null) protocolSubtype = ItemSubtype.getById(dc, SystemItems.getId(Protocol.EXTRACTION));
+    defaultProtocols = (List<Protocol>)activeProject.findDefaultItems(dc, protocolSubtype, false);
+  }
+
+  // Load recently used items
+  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL, currentSubtype);
+  List<Sample> recentSamples = (List<Sample>)cc.getRecent(dc, Item.SAMPLE);
+  List<BioPlate> recentBioPlates = (List<BioPlate>)cc.getRecent(dc, Item.BIOPLATE, currentSubtype);
+  List<Tag> recentTags = (List<Tag>)cc.getRecent(dc, Item.TAG, currentSubtype);
   
   // Query to retrieve item types
@@ -363 +380 @@
       }
       return parents;
+    }
+    
+    function subtypeOnChange()
+    {
+      var frm = document.forms['extract'];
+      var subtypeId = ItemSubtype.getSubtypeId('extract');
+      var recentInfo = ItemSubtype.getRecentAndRelatedInfo(subtypeId, 'EXTRACT', ['PROTOCOL', 'BIOPLATE', 'TAG', 'SAMPLE', 'EXTRACT']);
+      protocolChanged = ItemSubtype.updateRecentItemsInList(frm.protocol_id, recentInfo.PROTOCOL['recent']);
+      ItemSubtype.updateDefaultItemsInList(frm.protocol_id, recentInfo.PROTOCOL['default']);
+      ItemSubtype.updateRecentItemsInList(frm.tag_id, recentInfo.TAG['recent']);
+      ItemSubtype.updateRecentItemsInList(frm.bioplate_id, recentInfo.BIOPLATE['recent']);
     }
     
@@ -688 +716 @@
         <td colspan="2">
           <select name="subtype_id"
-            <%=!readCurrentSubtype ? "disabled readonly class=\"disabled selectionlist\"" : "class=\"selectionlist\""%>>
+            <%=!readCurrentSubtype ? "disabled readonly class=\"disabled selectionlist\"" : "class=\"selectionlist\""%>
+            onchange="subtypeOnChange()"
+            >
           <%
           if (!readCurrentSubtype)
@@ -701 +731 @@
             <option value="0">-none-
             <%
+            int currentSubtypeId = currentSubtype == null ? 0 : currentSubtype.getId();
             for (ItemSubtype subtype : subtypesQuery.list(dc))
             {
@@ -782 +813 @@
             denied="<%=!readCurrentProtocol%>"
             recent="<%=recentProtocols%>"
-            defaultitem="<%=defaultProtocol%>"
+            defaultitems="<%=defaultProtocols%>"
             newitem="<%=extract == null%>"
             onselect="selectProtocolOnClick()"

trunk/www/biomaterials/extracts/index.jsp

@@ -233 +233 @@
       extract.setOriginalQuantity(Values.getFloat(request.getParameter("original_quantity"), null));
       
+      int subtypeId = Values.getInt(request.getParameter("subtype_id"), -1);
+      ItemSubtype subtype = null;
+      if (subtypeId >= 0) // < 0 = denied or unchanged
+      {
+        if (subtypeId > 0) subtype = ItemSubtype.getById(dc, subtypeId);
+        extract.setItemSubtype(subtype);
+        if (subtype != null) cc.setRecent(subtype, maxRecent);
+      }
+      
       BioMaterialEvent creationEvent = extract.getCreationEvent();
       if (creationEvent.hasPermission(Permission.WRITE))
@@ -243 +252 @@
           Protocol pt = protocolId == 0 ? null : Protocol.getById(dc, protocolId);
           creationEvent.setProtocol(pt);
-          if (pt != null) cc.setRecent(pt, maxRecent);
+          if (pt != null) cc.setRecent(pt, subtype, maxRecent);
         }
-      }
-      
-      int subtypeId = Values.getInt(request.getParameter("subtype_id"), -1);
-      if (subtypeId >= 0) // < 0 = denied or unchanged
-      {
-        ItemSubtype subtype = subtypeId == 0 ? null : ItemSubtype.getById(dc, subtypeId);
-        extract.setItemSubtype(subtype);
-        if (subtype != null) cc.setRecent(subtype, maxRecent);
       }
       
@@ -260 +261 @@
         Tag tag = tagId == 0 ? null : Tag.getById(dc, tagId);
         extract.setTag(tag);
-        if (tag != null) cc.setRecent(tag, maxRecent);
+        if (tag != null) cc.setRecent(tag, subtype, maxRecent);
       }
 
@@ -274 +275 @@
         }
         extract.setBioWell(bw);
-        if (bw != null) cc.setRecent(bw.getPlate(), maxRecent);
+        if (bw != null) cc.setRecent(bw.getPlate(), subtype, maxRecent);
       }
   

trunk/www/biomaterials/samples/edit_sample.jsp

@@ -94 +94 @@
   boolean readCurrentProtocol = true;
   Protocol currentProtocol = null;
-  Protocol defaultProtocol = null;
   boolean readCurrentBioSource = true;
   BioSource currentBioSource = null;
@@ -107 +106 @@
   WellCoordinateFormatter columnFormatter = new WellCoordinateFormatter(false);
   
-  int activeProjectId = sc.getActiveProjectId();
-  if (activeProjectId > 0)
-  {
-    Project activeProject = Project.getById(dc, activeProjectId);
-    try
-    {
-      defaultProtocol = (Protocol)activeProject.findDefaultItem(dc, 
-          ItemSubtype.getById(dc, SystemItems.getId(Protocol.SAMPLING)), false);
-    }
-    catch(PermissionDeniedException pdex)
-    {
-      defaultProtocol = null;
-    }
-  }
-
   if (itemId == 0)
   {
@@ -250 +234 @@
   }
   
+  // Default items 
+  int activeProjectId = sc.getActiveProjectId();
+  List<Protocol> defaultProtocols = null;
+  if (activeProjectId > 0)
+  {
+    Project activeProject = Project.getById(dc, activeProjectId);
+    ItemSubtype protocolSubtype = currentSubtype == null ? null : currentSubtype.getRelatedSubtype(Item.PROTOCOL);
+    if (protocolSubtype == null) protocolSubtype = ItemSubtype.getById(dc, SystemItems.getId(Protocol.SAMPLING));
+    defaultProtocols = (List<Protocol>)activeProject.findDefaultItems(dc, protocolSubtype, false);
+  }
+  
   // Load recently used items
   List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL, currentSubtype);
   List<BioSource> recentBioSources = (List<BioSource>)cc.getRecent(dc, Item.BIOSOURCE);
-  List<BioPlate> recentBioPlates = (List<BioPlate>)cc.getRecent(dc, Item.BIOPLATE);
+  List<BioPlate> recentBioPlates = (List<BioPlate>)cc.getRecent(dc, Item.BIOPLATE, currentSubtype);
   
   // Query to retrieve item types
@@ -370 +365 @@
       var frm = document.forms['sample'];
       var subtypeId = ItemSubtype.getSubtypeId('sample');
-      var recentInfo = ItemSubtype.getRecentAndRelatedInfo(subtypeId, 'SAMPLE', ['PROTOCOL', 'BIOSOURCE', 'SAMPLE']);
-      protocolChanged = ItemSubtype.updateRecentItemsInList(frm.protocol_id, recentInfo.PROTOCOL.recent);
+      var recentInfo = ItemSubtype.getRecentAndRelatedInfo(subtypeId, 'SAMPLE', ['PROTOCOL', 'BIOPLATE', 'BIOSOURCE', 'SAMPLE']);
+      protocolChanged = ItemSubtype.updateRecentItemsInList(frm.protocol_id, recentInfo.PROTOCOL['recent']);
+      ItemSubtype.updateDefaultItemsInList(frm.protocol_id, recentInfo.PROTOCOL['default']);
+      ItemSubtype.updateRecentItemsInList(frm.bioplate_id, recentInfo.BIOPLATE['recent']);
     }
     
@@ -742 +739 @@
             denied="<%=!readCurrentProtocol%>"
             recent="<%=recentProtocols%>"
-            defaultitem="<%=defaultProtocol%>"
+            defaultitems="<%=defaultProtocols%>"
             newitem="<%=sample == null%>"
             onselect="selectProtocolOnClick()"

trunk/www/biomaterials/samples/index.jsp

@@ -263 +263 @@
         }
         sample.setBioWell(bw);
-        if (bw != null) cc.setRecent(bw.getPlate(), maxRecent);
+        if (bw != null) cc.setRecent(bw.getPlate(), subtype, maxRecent);
       }
   

trunk/www/include/scripts/subtypes.js

@@ -159 +159 @@
   this.updateRecentItemsInList = function(list, recentItems, noNoneOption)
   {
-    if (!list || !recentItems) return;
+    if (!list || !recentItems || !recentItems.length) return;
     
     var oldSelectedValue = list.selectedIndex >= 0 ? list[list.selectedIndex].value : 0;
@@ -211 +211 @@
   }
   
+  this.updateDefaultItemsInList = function(list, defaultItems, noNoneOption)
+  {
+    if (!list || !defaultItems || !defaultItems.length) return;
+    var defaultHeader = new Option('- project default -', 0);
+    defaultHeader.className = 'defaultheader';
+    defaultHeader.disabled = true;
+    list[list.length] = defaultHeader;
+    // Add the new items to the end of the list
+    for (var i = 0; i < defaultItems.length; i++)
+    {
+      list[list.length] = new Option(defaultItems[i].name, defaultItems[i].id);
+    }
+  }
 }
 

trunk/www/lims/arraybatches/edit_batch.jsp

@@ -74 +74 @@
   boolean readCurrentArrayDesign = true;
   ArrayDesign currentArrayDesign = null;
-  ArrayDesign defaultArrayDesign = null;
+  List<ArrayDesign> defaultArrayDesigns = null;
   boolean readCurrentProtocol = true;
   Protocol currentProtocol = null;
-  Protocol defaultProtocol = null;
+  List<Protocol> defaultProtocols = null;
   boolean readCurrentPrintRobot = true;
   Hardware currentPrintRobot = null;
-  Hardware defaultPrintRobot = null;
+  List<Hardware> defaultPrintRobots = null;
 
   // Load recently used items
@@ -93 +93 @@
     try
     {
-      defaultArrayDesign = (ArrayDesign)activeProject.findDefaultItem(dc, Item.ARRAYDESIGN);
+      defaultArrayDesigns = (List<ArrayDesign>)activeProject.findDefaultItems(dc, Item.ARRAYDESIGN, true);
     }
     catch (PermissionDeniedException pdex)
-    {
-      defaultArrayDesign = null;
-    }
-    try
-    {
-      defaultProtocol = (Protocol)activeProject.findDefaultItem(dc, 
+    {}
+    try
+    {
+      defaultProtocols = (List<Protocol>)activeProject.findDefaultItems(dc, 
           ItemSubtype.getById(dc, SystemItems.getId(Protocol.PRINTING)), false);
     }
     catch (PermissionDeniedException pdex)
-    {
-      defaultProtocol = null;
-    }
-    try
-    {
-      defaultPrintRobot = (Hardware)activeProject.findDefaultItem(dc, 
+    {}
+    try
+    {
+      defaultPrintRobots = (List<Hardware>)activeProject.findDefaultItems(dc, 
           ItemSubtype.getById(dc, SystemItems.getId(Hardware.PRINT_ROBOT)), false);
     }
     catch (PermissionDeniedException pdex)
-    {
-      defaultPrintRobot = null;
-    }
+    {}
   }
   if (itemId == 0)
@@ -404 +398 @@
               denied="<%=!readCurrentArrayDesign%>"
               recent="<%=recentArrayDesigns%>"
-              defaultitem="<%=defaultArrayDesign%>"
+              defaultitems="<%=defaultArrayDesigns%>"
               newitem="true"
               onselect="selectArrayDesignOnClick()"
@@ -424 +418 @@
             denied="<%=!readCurrentPrintRobot%>"
             recent="<%=recentPrintRobots%>"
-            defaultitem="<%=defaultPrintRobot%>"
+            defaultitems="<%=defaultPrintRobots%>"
             newitem="<%=batch == null%>"
             onselect="selectPrintRobotOnClick()"
@@ -440 +434 @@
             denied="<%=!readCurrentProtocol%>"
             recent="<%=recentProtocols%>"
-            defaultitem="<%=defaultProtocol%>"
+            defaultitems="<%=defaultProtocols%>"
             newitem="<%=batch == null%>"
             onselect="selectProtocolOnClick()"

trunk/www/lims/arraydesigns/edit_design.jsp

@@ -75 +75 @@
   Platform currentPlatform = null;
   PlatformVariant currentVariant = null;
-  Platform defaultPlatform = null;
-  PlatformVariant defaultVariant = null;
+  List<Platform> defaultPlatforms = null;
+  List<PlatformVariant> defaultVariants = null;
   
   int activeProjectId = sc.getActiveProjectId();
@@ -84 +84 @@
     try
     {
-      defaultPlatform = (Platform)activeProject.findDefaultItem(dc, Item.PLATFORM);
+      defaultPlatforms = (List<Platform>)activeProject.findDefaultItems(dc, Item.PLATFORM, true);
     }
     catch (PermissionDeniedException pdex)
@@ -90 +90 @@
     try
     {
-      defaultVariant = (PlatformVariant)activeProject.findDefaultItem(dc, Item.PLATFORMVARIANT);
+      defaultVariants = (List<PlatformVariant>)activeProject.findDefaultItems(dc, Item.PLATFORMVARIANT, true);
     }
     catch (PermissionDeniedException pdex)
@@ -109 +109 @@
     catch (Throwable t)
     {}
-    if (currentPlatform == null) currentPlatform = defaultPlatform;
-    if (currentVariant == null) currentVariant = defaultVariant;
+    if (currentPlatform == null && defaultPlatforms.size() > 0)
+    {
+      currentPlatform = defaultPlatforms.get(0);
+    }
+    if (currentVariant == null && defaultVariants.size() > 0)
+    {
+      currentVariant = defaultVariants.get(0);
+    }
   }
   else

trunk/www/views/derivedbioassays/edit_bioassay.jsp

@@ -30 +30 @@
   import="net.sf.basedb.core.Hardware"
   import="net.sf.basedb.core.Software"
+  import="net.sf.basedb.core.Project"
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ItemContext"
@@ -43 +44 @@
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.Values"
+  import="net.sf.basedb.util.ListUtil"
   import="net.sf.basedb.core.plugin.GuiContext"
   import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
@@ -50 +52 @@
   import="java.util.Date"
   import="java.util.List"
+  import="java.util.Collections"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
@@ -67 +70 @@
   
   boolean readCurrentSubtype = true;
-  int currentSubtypeId = 0;
+  ItemSubtype currentSubtype = null;
 
   boolean readCurrentPhysicalBioAssay = true;
@@ -80 +83 @@
   boolean readCurrentProtocol = true;
   Protocol currentProtocol = null;
-  Protocol defaultProtocol = null;
   
   boolean readCurrentHardware = true;
   Hardware currentHardware = null;
-  Hardware defaultHardware = null;
   
   boolean readCurrentSoftware = true;
   Software currentSoftware = null;
-  Software defaultSoftware = null;
-
-  // Load recently used items
-  List<PhysicalBioAssay> recentPhysicalBioAssays = (List<PhysicalBioAssay>)cc.getRecent(dc, Item.PHYSICALBIOASSAY);
-  List<DerivedBioAssay> recentParentBioAssays = (List<DerivedBioAssay>)cc.getRecent(dc, Item.DERIVEDBIOASSAY);
-  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL);
-  List<Hardware> recentHardware = (List<Hardware>)cc.getRecent(dc, Item.HARDWARE);
-  List<Software> recentSoftware = (List<Software>)cc.getRecent(dc, Item.SOFTWARE);
 
   if (itemId == 0)
@@ -101 +94 @@
     title = "New derived bioassay";
     cc.removeObject("item");
-    currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
-    if (currentSubtypeId == 0) 
-    {
-      int recentSubtypeId = Values.getInt(cc.getRecent(Item.ITEMSUBTYPE.name(), 0));
-      currentSubtypeId = Values.getInt(cc.getPropertyValue("itemSubtype"), recentSubtypeId);
-    }
-
+    int currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
+    List<ItemSubtype> relatedToParent = Collections.emptyList();
     int parentId = Values.getInt(request.getParameter("parent_id"));
     if (parentId != 0)
     {
       currentParentBioAssay = DerivedBioAssay.getById(dc, parentId);
+      if (currentSubtypeId == 0)
+      {
+        relatedToParent = ItemSubtype.getParentSubtypes(dc, currentParentBioAssay, Item.DERIVEDBIOASSAY);
+      }
       try
       {
@@ -133 +125 @@
       {
         currentPhysicalBioAssay = PhysicalBioAssay.getById(dc, physicalBioAssayId);
-      }
-    }
-    
+        if (currentSubtypeId == 0)
+        {
+          relatedToParent = ItemSubtype.getParentSubtypes(dc, currentPhysicalBioAssay, Item.DERIVEDBIOASSAY);
+        }
+      }
+    }
+    if (currentSubtypeId == 0) 
+    {
+      if (relatedToParent.size() > 0)
+      {
+        // Find most recently used related subtype
+        List<ItemSubtype> recentSubtypes = (List<ItemSubtype>)cc.getRecent(dc, Item.ITEMSUBTYPE);
+        currentSubtype = ListUtil.findFirstCommon(recentSubtypes, relatedToParent, relatedToParent.get(0));
+      }
+      else
+      {
+        int recentSubtypeId = Values.getInt(cc.getRecent(Item.ITEMSUBTYPE.name(), 0));
+        currentSubtypeId = Values.getInt(cc.getPropertyValue("itemSubtype"), recentSubtypeId);
+        if (currentSubtypeId > 0) currentSubtype = ItemSubtype.getById(dc, currentSubtypeId);
+      }
+    }
   }
   else
@@ -146 +156 @@
     try
     {
-      ItemSubtype subtype = bioAssay.getItemSubtype();
-      if (subtype != null) currentSubtypeId = subtype.getId();
+      currentSubtype = bioAssay.getItemSubtype();
     }
     catch (PermissionDeniedException ex)
@@ -202 +211 @@
     }
   }
+
+  // Default items 
+  int activeProjectId = sc.getActiveProjectId();
+  List<Protocol> defaultProtocols = null;
+  List<Hardware> defaultHardware = null;
+  List<Software> defaultSoftware = null;
+  if (activeProjectId > 0)
+  {
+    Project activeProject = Project.getById(dc, activeProjectId);
+    defaultProtocols = (List<Protocol>)activeProject.findDefaultItemsOfRelatedSubtype(dc, currentSubtype, Item.PROTOCOL);
+    defaultHardware = (List<Hardware>)activeProject.findDefaultItemsOfRelatedSubtype(dc, currentSubtype, Item.HARDWARE);
+    defaultSoftware = (List<Software>)activeProject.findDefaultItemsOfRelatedSubtype(dc, currentSubtype, Item.SOFTWARE);
+  }
+
+  // Load recently used items
+  List<PhysicalBioAssay> recentPhysicalBioAssays = (List<PhysicalBioAssay>)cc.getRecent(dc, Item.PHYSICALBIOASSAY);
+  List<DerivedBioAssay> recentParentBioAssays = (List<DerivedBioAssay>)cc.getRecent(dc, Item.DERIVEDBIOASSAY);
+  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL, currentSubtype);
+  List<Hardware> recentHardware = (List<Hardware>)cc.getRecent(dc, Item.HARDWARE, currentSubtype);
+  List<Software> recentSoftware = (List<Software>)cc.getRecent(dc, Item.SOFTWARE, currentSubtype);
+  
   // Query to retrieve item types
   final ItemQuery<ItemSubtype> subtypesQuery = Base.getSubtypesQuery(itemType);
@@ -346 +376 @@
     }
     
+    function subtypeOnChange()
+    {
+      var frm = document.forms['bioAssay'];
+      var subtypeId = ItemSubtype.getSubtypeId('bioAssay');
+      var recentInfo = ItemSubtype.getRecentAndRelatedInfo(subtypeId, 'BIOASSAY', ['PROTOCOL', 'HARDWARE', 'SOFTWARE']);
+      protocolChanged = ItemSubtype.updateRecentItemsInList(frm.protocol_id, recentInfo.PROTOCOL['recent']);
+      ItemSubtype.updateDefaultItemsInList(frm.protocol_id, recentInfo.PROTOCOL['default']);
+      ItemSubtype.updateRecentItemsInList(frm.hardware_id, recentInfo.HARDWARE['recent']);
+      ItemSubtype.updateDefaultItemsInList(frm.hardware_id, recentInfo.HARDWARE['default']);
+      ItemSubtype.updateRecentItemsInList(frm.software_id, recentInfo.SOFTWARE['recent']);
+      ItemSubtype.updateDefaultItemsInList(frm.software_id, recentInfo.SOFTWARE['default']);
+    }
+
+    
     function selectProtocolOnClick()
     {
       var frm = document.forms['bioAssay'];
-      var url = '../../../admin/protocols/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
+      var url = '../../admin/protocols/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
       url += '&callback=setProtocolCallback&resetTemporary=1';
       url += ItemSubtype.createRelatedFilter('bioAssay', 'PROTOCOL');
@@ -444 +488 @@
     {
       var frm = document.forms['bioAssay'];
-      var url = '../../../admin/hardware/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
+      var url = '../../admin/hardware/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
       url += '&callback=setHardwareCallback&resetTemporary=1';
       url += ItemSubtype.createRelatedFilter('bioAssay', 'HARDWARE');
@@ -469 +513 @@
     {
       var frm = document.forms['bioAssay'];
-      var url = '../../../admin/software/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
+      var url = '../../admin/software/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
       url += '&callback=setSoftwareCallback&resetTemporary=1';
       url += ItemSubtype.createRelatedFilter('bioAssay', 'SOFTWARE');
@@ -647 +691 @@
         <td colspan="2">
           <select name="subtype_id"
-            <%=!readCurrentSubtype ? "disabled readonly class=\"disabled selectionlist\"" : "class=\"selectionlist\""%>>
+            <%=!readCurrentSubtype ? "disabled readonly class=\"disabled selectionlist\"" : "class=\"selectionlist\""%>
+            onchange="subtypeOnChange()"
+            >
           <%
           if (!readCurrentSubtype)
@@ -660 +706 @@
             <option value="0">-none-
             <%
+            int currentSubtypeId = currentSubtype == null ? 0 : currentSubtype.getId();
             for (ItemSubtype subtype : subtypesQuery.list(dc))
             {
@@ -740 +787 @@
             denied="<%=!readCurrentProtocol%>"
             recent="<%=recentProtocols%>"
-            defaultitem="<%=defaultProtocol%>"
+            defaultitems="<%=defaultProtocols%>"
             newitem="<%=bioAssay == null%>"
             onselect="selectProtocolOnClick()"
@@ -757 +804 @@
             denied="<%=!readCurrentHardware%>"
             recent="<%=recentHardware%>"
-            defaultitem="<%=defaultHardware%>"
+            defaultitems="<%=defaultHardware%>"
             newitem="<%=bioAssay == null%>"
             onselect="selectHardwareOnClick()"
@@ -773 +820 @@
             denied="<%=!readCurrentSoftware%>"
             recent="<%=recentSoftware%>"
-            defaultitem="<%=defaultSoftware%>"
+            defaultitems="<%=defaultSoftware%>"
             newitem="<%=bioAssay == null%>"
             onselect="selectSoftwareOnClick()"

trunk/www/views/derivedbioassays/index.jsp

@@ -208 +208 @@
   
       int subtypeId = Values.getInt(request.getParameter("subtype_id"), -1);
+      ItemSubtype subtype = null;
       if (subtypeId >= 0) // < 0 = denied or unchanged
       {
-        ItemSubtype subtype = subtypeId == 0 ? null : ItemSubtype.getById(dc, subtypeId);
+        subtype = subtypeId == 0 ? null : ItemSubtype.getById(dc, subtypeId);
         bas.setItemSubtype(subtype);
         if (subtype != null) cc.setRecent(subtype, maxRecent);
@@ -227 +228 @@
         Protocol pt = protocolId == 0 ? null : Protocol.getById(dc, protocolId);
         bas.setProtocol(pt);
-        if (pt != null) cc.setRecent(pt, maxRecent);
+        if (pt != null) cc.setRecent(pt, subtype, maxRecent);
       }
       
@@ -235 +236 @@
         Hardware hw = hardwareId == 0 ? null : Hardware.getById(dc, hardwareId);
         bas.setHardware(hw);
-        if (hw != null) cc.setRecent(hw, maxRecent);
+        if (hw != null) cc.setRecent(hw, subtype, maxRecent);
       }
 
@@ -243 +244 @@
         Software sw = softwareId == 0 ? null : Software.getById(dc, softwareId);
         bas.setSoftware(sw);
-        if (sw != null) cc.setRecent(sw, maxRecent);
+        if (sw != null) cc.setRecent(sw, subtype, maxRecent);
       }
       

trunk/www/views/physicalbioassays/edit_bioassay.jsp

@@ -53 +53 @@
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.Values"
+  import="net.sf.basedb.util.ListUtil"
   import="net.sf.basedb.util.formatter.Formatter"
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
@@ -65 +66 @@
   import="java.util.HashSet"
   import="java.util.Date"
+  import="java.util.Collections"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
@@ -83 +85 @@
   BioMaterialEvent creationEvent = null;
   Date eventDate = null;
-  ItemQuery<Extract> extractsQuery = null;
+  List<Extract> parentExtracts = null;
   
   boolean readCurrentSubtype = true;
-  int currentSubtypeId = 0;
+  ItemSubtype currentSubtype = null;
   boolean readCurrentArraySlide = true;
   ArraySlide currentArraySlide = null;
@@ -92 +94 @@
   boolean readCurrentProtocol = true;
   Protocol currentProtocol = null;
-  Protocol defaultProtocol = null;
   
   boolean readCurrentHardware = true;
   Hardware currentHardware = null;
-  Hardware defaultHardware = null;
-
-  // Load recently used items
-  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL);
-  List<Hardware> recentHardware = (List<Hardware>)cc.getRecent(dc, Item.HARDWARE);
-  
-  int activeProjectId = sc.getActiveProjectId();
-  if (activeProjectId > 0)
-  {
-    Project activeProject = Project.getById(dc, activeProjectId);
-    try
-    {
-      defaultProtocol = (Protocol)activeProject.findDefaultItem(dc, 
-          ItemSubtype.getById(dc, SystemItems.getId(Protocol.HYBRIDIZATION)), false);
-    }
-    catch (PermissionDeniedException pdex)
-    {
-      defaultProtocol = null;
-    }
-    try
-    {
-      defaultHardware = (Hardware)activeProject.findDefaultItem(dc, 
-          ItemSubtype.getById(dc, SystemItems.getId(Hardware.HYBRIDIZATION_STATION)), false);
-    }
-    catch (PermissionDeniedException pdex)
-    {
-      defaultHardware = null;
-    }
-  }
+
   if (itemId == 0)
   {
     title = "Create physical bioassay";
     cc.removeObject("item");
-    currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
-    if (currentSubtypeId == 0) 
-    {
-      int recentSubtypeId = Values.getInt(cc.getRecent(Item.ITEMSUBTYPE.name(), 0));
-      currentSubtypeId = Values.getInt(cc.getPropertyValue("itemSubtype"), recentSubtypeId);
-    }
     if (cc.getPropertyFilter("creationEvent.protocol.name") != null)
     {
@@ -150 +117 @@
     eventDate = (Date)cc.getPropertyObject("creationEvent.eventDate");
     
+    int currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
+    List<ItemSubtype> relatedToParent = Collections.emptyList();
+    ItemQuery<Extract> extractsQuery = null;
     if (Values.getBoolean(request.getParameter("useParents")))
     {
@@ -169 +139 @@
       extractsQuery.restrict(Restrictions.eq(Hql.property("id"), 
         Expressions.integer(leId)));
+    }
+    
+    if (extractsQuery != null)
+    {
+      parentExtracts = extractsQuery.list(dc);
+      if (currentSubtypeId == 0 && parentExtracts.size() > 0)
+      {
+        relatedToParent = ItemSubtype.getParentSubtypes(dc, parentExtracts.get(0), Item.PHYSICALBIOASSAY);
+      }
+    }
+    
+    if (currentSubtypeId == 0) 
+    {
+      if (relatedToParent.size() > 0)
+      {
+        // Find most recently used related subtype
+        List<ItemSubtype> recentSubtypes = (List<ItemSubtype>)cc.getRecent(dc, Item.ITEMSUBTYPE);
+        currentSubtype = ListUtil.findFirstCommon(recentSubtypes, relatedToParent, relatedToParent.get(0));
+      }
+      else
+      {
+        int recentSubtypeId = Values.getInt(cc.getRecent(Item.ITEMSUBTYPE.name(), 0));
+        currentSubtypeId = Values.getInt(cc.getPropertyValue("itemSubtype"), recentSubtypeId);
+        if (currentSubtypeId > 0) currentSubtype = ItemSubtype.getById(dc, currentSubtypeId);
+      }
     }
   }
@@ -183 +178 @@
     try
     {
-      ItemSubtype subtype = pba.getItemSubtype();
-      if (subtype != null) currentSubtypeId = subtype.getId();
+      currentSubtype = pba.getItemSubtype();
     }
     catch (PermissionDeniedException ex)
@@ -217 +211 @@
     
     // Query to retrieve source extracts
-    extractsQuery = (ItemQuery<Extract>)creationEvent.getSources();
+    ItemQuery<Extract> extractsQuery = (ItemQuery<Extract>)creationEvent.getSources();
     extractsQuery.include(Include.ALL);
     extractsQuery.order(Orders.asc(Hql.property("name")));
+    parentExtracts = extractsQuery.list(dc);
     
   }
+  
+  // Default items 
+  int activeProjectId = sc.getActiveProjectId();
+  List<Protocol> defaultProtocols = null;
+  List<Hardware> defaultHardware = null;
+  if (activeProjectId > 0)
+  {
+    Project activeProject = Project.getById(dc, activeProjectId);
+    defaultProtocols = (List<Protocol>)activeProject.findDefaultItemsOfRelatedSubtype(dc, currentSubtype, Item.PROTOCOL);
+    defaultHardware = (List<Hardware>)activeProject.findDefaultItemsOfRelatedSubtype(dc, currentSubtype, Item.HARDWARE);
+  }
+  
+  // Load recently used items
+  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL, currentSubtype);
+  List<Hardware> recentHardware = (List<Hardware>)cc.getRecent(dc, Item.HARDWARE, currentSubtype);
+  
   // Query to retrieve item types
   final ItemQuery<ItemSubtype> subtypesQuery = Base.getSubtypesQuery(itemType);
@@ -319 +330 @@
       return protocolId;
     }
-
+    
     function getParents()
     {
@@ -336 +347 @@
     }
 
+    function subtypeOnChange()
+    {
+      var frm = document.forms['bioassay'];
+      var subtypeId = ItemSubtype.getSubtypeId('bioassay');
+      var recentInfo = ItemSubtype.getRecentAndRelatedInfo(subtypeId, 'BIOASSAY', ['PROTOCOL', 'HARDWARE']);
+      protocolChanged = ItemSubtype.updateRecentItemsInList(frm.protocol_id, recentInfo.PROTOCOL['recent']);
+      ItemSubtype.updateDefaultItemsInList(frm.protocol_id, recentInfo.PROTOCOL['default']);
+      ItemSubtype.updateRecentItemsInList(frm.hardware_id, recentInfo.HARDWARE['recent']);
+      ItemSubtype.updateDefaultItemsInList(frm.hardware_id, recentInfo.HARDWARE['default']);
+    }
+    
     function selectProtocolOnClick()
     {
@@ -541 +563 @@
         <%
       }
-      if (extractsQuery != null)
-      {
-        ItemResultList<Extract> extracts = extractsQuery.list(dc);
-        for (Extract extract : extracts)
+      if (parentExtracts != null)
+      {
+        for (Extract extract : parentExtracts)
         {
           if (pba == null)
@@ -590 +611 @@
         <td colspan="2">
           <select name="subtype_id"
-            <%=!readCurrentSubtype ? "disabled readonly class=\"disabled selectionlist\"" : "class=\"selectionlist\""%>>
+            <%=!readCurrentSubtype ? "disabled readonly class=\"disabled selectionlist\"" : "class=\"selectionlist\""%>
+            onchange="subtypeOnChange()"
+            >
           <%
           if (!readCurrentSubtype)
@@ -600 +623 @@
           else
           {
+            int currentSubtypeId = currentSubtype == null ? 0 : currentSubtype.getId();
             %>
             <option value="0">-none-
@@ -662 +686 @@
             denied="<%=!readCurrentProtocol%>"
             recent="<%=recentProtocols%>"
-            defaultitem="<%=defaultProtocol%>"
+            defaultitems="<%=defaultProtocols%>"
             newitem="<%=pba == null%>"
             onselect="selectProtocolOnClick()"
@@ -679 +703 @@
             denied="<%=!readCurrentHardware%>"
             recent="<%=recentHardware%>"
-            defaultitem="<%=defaultHardware%>"
+            defaultitems="<%=defaultHardware%>"
             newitem="<%=pba == null%>"
             onselect="selectHardwareOnClick()"

trunk/www/views/physicalbioassays/index.jsp

@@ -198 +198 @@
       pba.setDescription(Values.getStringOrNull(request.getParameter("description")));
       pba.setSize(Values.getInt(request.getParameter("size"), 1));
+
+      int subtypeId = Values.getInt(request.getParameter("subtype_id"), -1);
+      ItemSubtype subtype = null;
+      if (subtypeId >= 0) // < 0 = denied or unchanged
+      {
+        if (subtypeId > 0) subtype = ItemSubtype.getById(dc, subtypeId);
+        pba.setItemSubtype(subtype);
+        if (subtype != null) cc.setRecent(subtype, maxRecent);
+      }
       
       int arraySlideId = Values.getInt(request.getParameter("arrayslide_id"), -1);
@@ -212 +221 @@
         Protocol pt = protocolId == 0 ? null : Protocol.getById(dc, protocolId);
         creationEvent.setProtocol(pt);
-        if (pt != null) cc.setRecent(pt, maxRecent);
+        if (pt != null) cc.setRecent(pt, subtype, maxRecent);
       }
       
-      int subtypeId = Values.getInt(request.getParameter("subtype_id"), -1);
-      if (subtypeId >= 0) // < 0 = denied or unchanged
-      {
-        ItemSubtype subtype = subtypeId == 0 ? null : ItemSubtype.getById(dc, subtypeId);
-        pba.setItemSubtype(subtype);
-        if (subtype != null) cc.setRecent(subtype, maxRecent);
-      }
-
       //Hardware
       int hardwareId = Values.getInt(request.getParameter("hardware_id"), -1);
@@ -229 +230 @@
         Hardware hw = hardwareId == 0 ? null : Hardware.getById(dc, hardwareId);
         creationEvent.setHardware(hw);
-        if (hw != null) cc.setRecent(hw, maxRecent);
+        if (hw != null) cc.setRecent(hw, subtype, maxRecent);
       }
       

trunk/www/views/rawbioassays/edit_rawbioassay.jsp

@@ -85 +85 @@
   boolean deniedPlatform = false;
   Platform currentPlatform = null;
-  Platform defaultPlatform = null;
+  List<Platform> defaultPlatforms = null;
   PlatformVariant currentVariant = null;
-  PlatformVariant defaultVariant = null;
+  List<PlatformVariant> defaultVariants = null;
   
   boolean readCurrentBioAssay = true;
@@ -95 +95 @@
   boolean readCurrentProtocol = true;
   Protocol currentProtocol = null;
-  Protocol defaultProtocol = null;
+  List<Protocol> defaultProtocols = null;
   boolean readCurrentSoftware = true;
   Software currentSoftware = null;
-  Software defaultSoftware = null;
+  List<Software> defaultSoftware = null;
   boolean readCurrentArrayDesign = true;
   ArrayDesign currentArrayDesign = null;
-  ArrayDesign defaultArrayDesign = null;
+  List<ArrayDesign> defaultArrayDesigns = null;
   RawDataType currentRawDataType = null;
   RawDataType defaultRawDataType = null;
@@ -119 +119 @@
     try
     {
-      defaultProtocol = (Protocol)activeProject.findDefaultItem(dc, 
+      defaultProtocols = (List<Protocol>)activeProject.findDefaultItems(dc, 
           ItemSubtype.getById(dc, SystemItems.getId(Protocol.FEATURE_EXTRACTION)), false);
-    }
-    catch (PermissionDeniedException pdex)
-    {
-      defaultProtocol = null;
-    }
-    try
-    {
-      defaultSoftware = (Software)activeProject.findDefaultItem(dc, 
-          ItemSubtype.getById(dc, SystemItems.getId(Software.FEATURE_EXTRACTION)), false);
-    }
-    catch (PermissionDeniedException pdex)
-    {
-      defaultSoftware = null;
-    }
-    try
-    {
-      defaultArrayDesign = (ArrayDesign)activeProject.findDefaultItem(dc, Item.ARRAYDESIGN);
-    }
-    catch (PermissionDeniedException pdex)
-    {
-      defaultArrayDesign = null;
-    }
-    try
-    {
-      defaultPlatform = (Platform)activeProject.findDefaultItem(dc, Item.PLATFORM);
     }
     catch (PermissionDeniedException pdex)
@@ -151 +126 @@
     try
     {
-      defaultVariant = (PlatformVariant)activeProject.findDefaultItem(dc, Item.PLATFORMVARIANT);
+      defaultSoftware = (List<Software>)activeProject.findDefaultItems(dc, 
+          ItemSubtype.getById(dc, SystemItems.getId(Software.FEATURE_EXTRACTION)), false);
+    }
+    catch (PermissionDeniedException pdex)
+    {}
+    try
+    {
+      defaultArrayDesigns = (List<ArrayDesign>)activeProject.findDefaultItems(dc, Item.ARRAYDESIGN, true);
+    }
+    catch (PermissionDeniedException pdex)
+    {}
+    try
+    {
+      defaultPlatforms = (List<Platform>)activeProject.findDefaultItems(dc, Item.PLATFORM, true);
+    }
+    catch (PermissionDeniedException pdex)
+    {}
+    try
+    {
+      defaultVariants = (List<PlatformVariant>)activeProject.findDefaultItems(dc, Item.PLATFORMVARIANT, true);
     }
     catch (PermissionDeniedException pdex)
@@ -176 +170 @@
     catch (Throwable t)
     {}
-    if (currentPlatform == null) currentPlatform = defaultPlatform;
-    if (currentVariant == null) currentVariant = defaultVariant;
+    if (currentPlatform == null && defaultPlatforms.size() > 0) 
+    {
+      currentPlatform = defaultPlatforms.get(0);
+    }
+    if (currentVariant == null && defaultVariants.size() > 0)
+    {
+      currentVariant = defaultVariants.get(0);
+    }
     
     currentRawDataType = RawDataTypes.getRawDataType(cc.getPropertyValue("rawDataType"));
@@ -772 +772 @@
             denied="<%=!readCurrentArrayDesign%>"
             recent="<%=recentArrayDesigns%>"
-            defaultitem="<%=defaultArrayDesign%>"
+            defaultitems="<%=defaultArrayDesigns%>"
             newitem="<%=rawBioAssay == null%>"
             onselect="selectArrayDesignOnClick()"
@@ -804 +804 @@
             denied="<%=!readCurrentProtocol%>"
             recent="<%=recentProtocols%>"
-            defaultitem="<%=defaultProtocol%>"
+            defaultitems="<%=defaultProtocols%>"
             newitem="<%=rawBioAssay == null%>"
             onselect="selectProtocolOnClick()"
@@ -821 +821 @@
             denied="<%=!readCurrentSoftware%>"
             recent="<%=recentSoftware%>"
-            defaultitem="<%=defaultSoftware%>"
+            defaultitems="<%=defaultSoftware%>"
             newitem="<%=rawBioAssay == null%>"
             onselect="selectSoftwareOnClick()"