Changeset 5686

Timestamp:

Aug 5, 2011, 2:54:06 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1597: Subtypes of items

Smarter selection of default subtypes and related items (protocols, etc) when new items are created. The 'recently used items' are remembered per subtype so the list should contain more relevant entries when creating items of different subtypes.

Implemented by the sample edit dialog so far. The current implementation more or less prevents the use of project default items (which also depend on the subtype). This need to be fixed and integrate into the current solution.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/ItemContext.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/ItemSubtype.java (modified) (3 diffs)
• src/core/net/sf/basedb/util/ListUtil.java (added)
• www/admin/itemsubtypes/ajax.jsp (modified) (3 diffs)
• www/admin/itemsubtypes/list_subtypes.jsp (modified) (3 diffs)
• www/biomaterials/samples/edit_sample.jsp (modified) (15 diffs)
• www/biomaterials/samples/index.jsp (modified) (2 diffs)
• www/include/scripts/subtypes.js (modified) (3 diffs)

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

@@ -727 +727 @@
   
   /**
+    Add an item to the "recently used items" list when used for a specific
+    item subtype. Each type of item+subtype has their own list which may contain at 
+    most <code>maxInList</code> items. 
+    <p>
+    Note! The lists are stored as string of colon-separated ID:s in
+    the setting given by the item type. For example the recently used
+    protocols are found in the setting: 
+    <code>getSetting("PROTOCOL.#subtype-id.recent")</code>. Client code is advised to
+    not change these settings.
+    
+    @param item The item to add
+    @param subtype The subtype of the parent item (can be null)
+    @param maxInList The maximum number of items in the list
+    @since 3.0
+   */
+  public void setRecent(BasicItem item, ItemSubtype subtype, int maxInList)
+  {
+    if (subtype == null)
+    {
+      setRecent(item, maxInList);
+    }
+    else
+    {
+      setRecent(item, "#"+subtype.getId(), maxInList);
+    }
+  }
+  
+  /**
     Add an item to the "recently used items" list. Each type of item
     has their own list and sublists which may contain at 
@@ -783 +811 @@
   
   /**
+    Get the number of recently used items in the list.
+    @param itemType The type of items
+    @param subtype The subtype of the parent item (can be null)
+    @since 3.0
+  */
+  public int getNumRecent(Item itemType, ItemSubtype subtype)
+  {
+    if (subtype == null)
+    {
+      return getNumRecent(itemType);
+    }
+    else
+    {
+      return getNumRecent(itemType, "#"+subtype.getId());
+    }
+  }
+  
+  /**
     Get the number of recently used items in a list with a sublist.
     @param itemType The type of items
@@ -816 +862 @@
   {
     return loadRecent(dc, itemType, itemType.name());
+  }
+  
+  /**
+    Get all recently used items of the specified type. The list
+    only contains items that the logged in user has read permission
+    to and that hasn't been deleted. Thus, the {@link #getNumRecent(Item, ItemSubtype)}
+    may return a larger number than what is actually returned in this
+    list.
+    
+    @param dc The DbControl used to access the database
+    @param itemType The type of items
+    @param subtype The subtype of the parent item (can be null)
+    @return A list with the items
+    @since 3.0
+  */
+  public List<? extends BasicItem> getRecent(DbControl dc, Item itemType, ItemSubtype subtype)
+  {
+    if (subtype == null)
+    {
+      return getRecent(dc, itemType);
+    }
+    else
+    {
+      return getRecent(dc, itemType, "#" + subtype.getId());
+    }
   }
   
@@ -923 +994 @@
     setRecent(itemType.name(), null);
   }
-  
+
+  /**
+    Clear the recently used items list from items of the specified type.
+    @param itemType The type of items
+    @param subtype The subtype of the parent item (can be null)
+    @since 3.0
+  */
+  public void clearRecent(Item itemType, ItemSubtype subtype)
+  {
+    if (subtype == null)
+    {
+      clearRecent(itemType);
+    }
+    else
+    {
+      clearRecent(itemType, "#" + subtype.getId());
+    }
+  }
+  
+
   /**
     Clear the recently used items sublist from items of the specified type.

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

@@ -35 +35 @@
 import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.util.ClassUtil;
@@ -121 +122 @@
   /**
     Utility method for loading a subtype that is related to the subtype of the given item.
+    This is more or less equivalent to calling {@link Subtypable#getItemSubtype()} and
+    then {@link ItemSubtype#getRelatedSubtype(Item)} but with proper null handling and
+    a possibility to return a default subtype if no related one can be found.
+    
     @param dc A DbControl to use for database access
     @param item A subtypable item
@@ -172 +177 @@
     
     return null;
+  }
+  
+  /**
+    Utility method for locating all subtypes that have a relationship to the
+    subtype of the given item. This is more or less equivalent to finding
+    all subtypes were the method {@link ItemSubtype#getRelatedSubtype(Item)}
+    return the subtype of the given subtypable item (optionally restricting
+    to one parent item type).
+    
+    @param dc A DbControl to use for database access
+    @param item A subtypeable item
+    @param parentType The item type of the subtypes that we want to find or null
+      to find any subtype
+    @return A list with the subtypes, or an empty list if none could be found
+  */
+  public static List<ItemSubtype> getParentSubtypes(DbControl dc, Subtypable item, Item parentType)
+  {
+    ItemSubtype subtype = item.getItemSubtype();
+    if (subtype == null) return Collections.emptyList();
+    
+    ItemQuery<ItemSubtype> query = subtype.getParentSubtypes();
+    if (parentType != null)
+    {
+      query.restrict(Restrictions.eq(Hql.property("itemType"), Expressions.integer(parentType.getValue())));
+    }
+    query.order(Orders.asc(Hql.property("name")));
+    return query.list(dc);
   }
   

trunk/www/admin/itemsubtypes/ajax.jsp

@@ -26 +26 @@
   import="net.sf.basedb.core.DbControl"
   import="net.sf.basedb.core.Item"
+  import="net.sf.basedb.core.ItemContext"
   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.InvalidDataException"
   import="net.sf.basedb.util.Values"
@@ -34 +37 @@
   import="net.sf.basedb.clients.web.WebException"
   import="org.json.simple.JSONObject"
+  import="org.json.simple.JSONArray"
+  import="java.util.List"
 %>
 <%
@@ -82 +87 @@
     dc.close();
   }
+  else if ("GetRecentAndRelated".equals(cmd))
+  {
+    dc = sc.newDbControl();
+
+    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);
+
+    if (subtype != null)
+    {
+      json.put("id", subtype.getId());
+      json.put("name", subtype.getName());
+    }
+    
+    for (String relatedType : request.getParameterValues("relatedType"))
+    {
+      JSONObject jsonITEM = new JSONObject();
+      Item relatedItem = Item.valueOf(relatedType);
+      
+      // Load the related subtype
+      if (subtype != null)
+      {
+        ItemSubtype relatedSubtype = subtype.getRelatedSubtype(relatedItem);
+        if (relatedSubtype != null)
+        {
+          JSONObject jsonRelated = new JSONObject();
+          jsonRelated.put("id", relatedSubtype.getId());
+          jsonRelated.put("name", relatedSubtype.getName());
+          jsonITEM.put("related", jsonRelated);
+        }
+      }
+      
+      // Load the most recently used items
+      List<? extends BasicItem> recentItems = cc.getRecent(dc, relatedItem, subtype);
+      if (recentItems != null && recentItems.size() > 0)
+      {
+        JSONArray jsonRecent = new JSONArray();
+        for (BasicItem recent : recentItems)
+        {
+          JSONObject jsonRecentItem = new JSONObject();
+          jsonRecentItem.put("id", recent.getId());
+          jsonRecentItem.put("name", ((Nameable)recent).getName());
+          jsonRecent.add(jsonRecentItem);
+        }
+        jsonITEM.put("recent", jsonRecent);
+      }
+      json.put(relatedType, jsonITEM);
+    }
+    dc.close();
+  }
   else
   {

trunk/www/admin/itemsubtypes/list_subtypes.jsp

@@ -92 +92 @@
   Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
 
+  ItemQuery<ItemSubtype> relatedQuery = ItemSubtype.getQuery(null);
+  relatedQuery.join(Hql.innerJoin("parents", "pp"));
+  relatedQuery.restrict(Restrictions.eq(Hql.alias("pp"), Hql.entityParameter("subtype", Item.ITEMSUBTYPE)));
+  relatedQuery.order(Orders.asc(Hql.property("name")));
+  relatedQuery.include(cc.getInclude());
+  
   Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
   try
@@ -258 +264 @@
         exportable="true"
       />
+      <tbl:columndef 
+        id="relatedTypes"
+        property="&relatedSubtypes(name)"
+        datatype="string"
+        title="Related item types"
+        filterable="true"
+        exportable="true"
+      />      
       <tbl:columndef 
         id="description"
@@ -423 +437 @@
                 <tbl:cell column="systemId"><%=Values.getString(item.getSystemId())%></tbl:cell>
                 <tbl:cell column="itemType"><%=item.getMainItemType()%></tbl:cell>
+                <tbl:cell column="relatedTypes">
+                  <%
+                  relatedQuery.setEntityParameter("subtype", item);
+                  String separator = "";
+                  for (ItemSubtype related : relatedQuery.list(dc))
+                  {
+                    out.write(separator);
+                    if (mode.hasPropertyLink())
+                    {
+                      out.write(Base.getLinkedName(ID, related, false, mode.hasEditLink()));
+                    }
+                    else
+                    {
+                      out.write(HTML.encodeTags(related.getName()));
+                    }
+                    out.write(" (" + related.getMainItemType() + ")");
+                    separator = ", ";
+                  }
+                  %>
+                </tbl:cell>
                 <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
               </tbl:row>

trunk/www/biomaterials/samples/edit_sample.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.WellCoordinateFormatter"
   import="net.sf.basedb.util.formatter.Formatter"
@@ -66 +67 @@
   import="java.util.HashSet"
   import="java.util.Date"
+  import="java.util.Collections"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
@@ -89 +91 @@
 
   boolean readCurrentSubtype = true;
-  int currentSubtypeId = 0;
+  ItemSubtype currentSubtype = null;
   boolean readCurrentProtocol = true;
   Protocol currentProtocol = null;
@@ -102 +104 @@
   BioPlate currentBioPlate = null;
   
-  // Load recently used items
-  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL);
-  List<BioSource> recentBioSources = (List<BioSource>)cc.getRecent(dc, Item.BIOSOURCE);
-  List<BioPlate> recentBioPlates = (List<BioPlate>)cc.getRecent(dc, Item.BIOPLATE);
-  
   WellCoordinateFormatter rowFormatter = new WellCoordinateFormatter(true);
   WellCoordinateFormatter columnFormatter = new WellCoordinateFormatter(false);
@@ -124 +121 @@
     }
   }
-    
 
   if (itemId == 0)
@@ -130 +126 @@
     title = "Create sample";
     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)
     {
@@ -142 +132 @@
     int bioSourceId = Values.getInt(request.getParameter("biosource_id"));
     int sampleId = Values.getInt(request.getParameter("sample_id"));
+    int currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
+    List<ItemSubtype> relatedToParent = Collections.emptyList();
     if (bioSourceId != 0)
     {
@@ -147 +139 @@
       parentType = Item.BIOSOURCE;
       name = currentBioSource.getName() + ".s" + (currentBioSource.countSamples() + 1);
+      if (currentSubtypeId == 0)
+      {
+        relatedToParent = ItemSubtype.getParentSubtypes(dc, currentBioSource, Item.SAMPLE);
+      }
     }
     else if (sampleId != 0)
@@ -155 +151 @@
       samplesQuery = Sample.getQuery();
       samplesQuery.restrict(Restrictions.eq(Hql.property("id"), Expressions.integer(sampleId)));
+      if (currentSubtypeId == 0)
+      {
+        relatedToParent = ItemSubtype.getParentSubtypes(dc, s, Item.SAMPLE);
+      }
     }
     else if (Values.getBoolean(request.getParameter("pooled")))
@@ -167 +167 @@
     {
       name = Values.getString(cc.getPropertyValue("name"), "New sample");
+    }
+    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");
@@ -185 +200 @@
     try
     {
-      ItemSubtype subtype = sample.getItemSubtype();
-      if (subtype != null) currentSubtypeId = subtype.getId();
+      currentSubtype = sample.getItemSubtype();
     }
     catch (PermissionDeniedException ex)
@@ -235 +249 @@
     }
   }
+  
+  // 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);
   
   // Query to retrieve item types
@@ -347 +366 @@
     }
     
+    function subtypeOnChange()
+    {
+      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);
+    }
+    
     function selectProtocolOnClick()
     {
@@ -633 +660 @@
         <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)
@@ -646 +675 @@
             <option value="0">-none-
             <%
+            int currentSubtypeId = currentSubtype == null ? 0 : currentSubtype.getId();
             for (ItemSubtype subtype : subtypesQuery.list(dc))
             {

trunk/www/biomaterials/samples/index.jsp

@@ -228 +228 @@
       sample.setExternalId(Values.getStringOrNull(request.getParameter("external_id")));
       sample.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);
+        sample.setItemSubtype(subtype);
+        if (subtype != null) cc.setRecent(subtype, maxRecent);
+      }
       
       BioMaterialEvent creationEvent = sample.getCreationEvent();
@@ -239 +248 @@
           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);
-        sample.setItemSubtype(subtype);
-        if (subtype != null) cc.setRecent(subtype, maxRecent);
-      }
-      
+  
       int biowellId = Values.getInt(request.getParameter("biowell_id"), -1);
       if (biowellId >= 0) // < 0 = denied or unchanged

trunk/www/include/scripts/subtypes.js

@@ -28 +28 @@
 function ItemSubtypeClass()
 {
+  
+  this.cache = new Array();
+  
   /**
     Get the subtype of the given item.
@@ -62 +65 @@
       return null;
     }
+    
+    // Use cached information if we have it
+    var info = this.cache['ID'+subtypeId];
+    if (info && info[relatedItemType] && info[relatedItemType].related)
+    {
+      return info[relatedItemType].related;
+    }
+    
     var request = Ajax.getXmlHttpRequest();
     var ID = getSessionId();
@@ -97 +108 @@
   }
   
+  this.getRecentAndRelatedInfo = function(subtypeId, mainItemType, relatedItemTypes)
+  {
+    var info = this.cache['ID' + subtypeId];
+    if (info)
+    {
+      // We have some info already, but...
+      // ...check if we are missing info about some related item types
+      var missingInfo = new Array();
+      for (var i = 0; i < relatedItemTypes.length; i++)
+      {
+        if (!info[relatedItemTypes[i]]) missingInfo[missingInfo.length] = relatedItemTypes[i];
+      }
+      relatedItemTypes = missingInfo;
+    }
+    
+    // Get more info...
+    if (relatedItemTypes.length > 0)
+    {
+      var request = Ajax.getXmlHttpRequest();
+      var url = getRoot() + 'admin/itemsubtypes/ajax.jsp?ID=' + getSessionId();
+      url += '&cmd=GetRecentAndRelated&itemType='+mainItemType;
+      if (subtypeId) 
+      {
+        url += '&item_id='+subtypeId;
+      }
+      for (var i = 0; i < relatedItemTypes.length; i++)
+      {
+        url += '&relatedType=' + relatedItemTypes[i];
+      }
+      request.open("GET", url, false); 
+      request.send(null);
+      var moreInfo = JSON.parse(request.responseText);
+      if (!info)
+      {
+        info = moreInfo;
+      }
+      else
+      {
+        // Merge the new info with the existing info
+        for (var i = 0; i < relatedItemTypes.length; i++)
+        {
+          info[relatedItemTypes[i]]= moreInfo[relatedItemTypes[i]];
+        }
+      }
+      this.cache['ID'+subtypeId] = info;
+    }
+    return info;
+  }
+  
+  this.updateRecentItemsInList = function(list, recentItems, noNoneOption)
+  {
+    if (!list || !recentItems) return;
+    
+    var oldSelectedValue = list.selectedIndex >= 0 ? list[list.selectedIndex].value : 0;
+    var reselectItemId = 0;
+    
+    // Find the current 'recently used' option in the list
+    // It should be the first entry which has a value == 0
+    // ignoring the 'none' option if present
+    var recentHeaderIndex = -1;
+    for (var i = noNoneOption ? 0 : 1; i < list.length; i++)
+    {
+      if (list[i].value == 0)
+      {
+        // Found it -- remove all items below it 
+        // but remember the ID of the currently selected 
+        // item if it is removed (so we can select it again)
+        recentHeaderIndex = i;
+        if (list.selectedIndex > i) 
+        {
+          reselectItemId = list[list.selectedIndex].value;
+        }
+        list.length = i+1;
+      }
+    }
+    
+    // If index == -1 we didn't find it so we must add 'recently used'
+    if (recentHeaderIndex == -1)
+    {
+      var recentHeader = new Option('- recently used -', 0);
+      recentHeader.className = 'recentheader';
+      recentHeader.disabled = true;
+      recentHeaderIndex = list.length;
+      list[recentHeaderIndex] = recentHeader;
+    }
+    
+    // Add the new items to the end of the list
+    for (var i = 0; i < recentItems.length; i++)
+    {
+      var selected = reselectItemId == recentItems[i].id;
+      list[list.length] = new Option((i+1) + '. ' + recentItems[i].name, recentItems[i].id, false, selected);
+    }
+    
+    // If no item is selected, select the first 'recently used' item.
+    if (list.selectedIndex == 0) 
+    {
+      list.selectedIndex = recentHeaderIndex+1;
+    }
+    
+    var currentSelectedValue = list.selectedIndex >= 0 ? list[list.selectedIndex].value : 0;
+    return oldSelectedValue != currentSelectedValue;
+  }
   
 }