Changeset 6994

Timestamp:

Nov 3, 2015, 9:47:41 AM (7 years ago)

Author:

Nicklas Nordborg

Message:

References #1958: Add Kit item

Kits can now be selected for physical bioassays.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/Install.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/Kit.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PhysicalBioAssay.java (modified) (1 diff)
• www/views/physicalbioassays/bioassays.js (modified) (2 diffs)
• www/views/physicalbioassays/edit_bioassay.jsp (modified) (6 diffs)
• www/views/physicalbioassays/index.jsp (modified) (2 diffs)
• www/views/physicalbioassays/list_bioassays.jsp (modified) (2 diffs)
• www/views/physicalbioassays/view_bioassay.jsp (modified) (1 diff)

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

@@ -480 +480 @@
       ItemSubtypeData libraryPrepKit = createItemSubtype(Item.KIT, Kit.LIBRARY_PREPARATION, 
           "Library preparation", "Kits used for creating libraries.");
+      ItemSubtypeData hybKit = createItemSubtype(Item.KIT, Kit.HYBRIDIZATION, 
+          "Hybridization", "Kits used for creating hybridizations.");
+      ItemSubtypeData clusterKit = createItemSubtype(Item.KIT, Kit.CLUSTER_GENERATION, 
+          "Cluster generation", "Kits used for cluster generation in a flow cell");
 
       // Hardware subtypes
@@ -518 +522 @@
       ItemSubtypeData hybridization = createItemSubtype(Item.PHYSICALBIOASSAY, PhysicalBioAssay.HYBRIDIZATION, 
         "Hybridization", "A bioassay representing a microarray slide with labeled extracts.", 
-        hybProtocol, hybStation, labeledExtract);
+        hybProtocol, hybStation, hybKit, labeledExtract);
       ItemSubtypeData clonalAmplification = createItemSubtype(Item.PHYSICALBIOASSAY, PhysicalBioAssay.CLONAL_AMPLIFICATION, 
-        "Clonal amplification", "A bioassay representing extracts that has been amplified in preparation for sequencing.", clusterProtocol, clusterGenerator, library);
+        "Clonal amplification", "A bioassay representing extracts that has been amplified in preparation for sequencing.", 
+        clusterProtocol, clusterGenerator, clusterKit, library);
       
       // Derived bioassay set subtypes

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

@@ -72 +72 @@
   public static final String LIBRARY_PREPARATION = "net.sf.basedb.core.KitType.LIBRARY_PREPARATION";
   
+  /**
+    The ID for the hybridization kit type, for example a kit
+    used when creating a {@link PhysicalBioAssay} from a set of
+    (labeled) {@link Extract}:s.
+  */
+  public static final String HYBRIDIZATION = "net.sf.basedb.core.KitType.HYBRIDIZATION";
+  
+  /**
+    The ID for the cluster generation (in a flow cell) kit type, for example 
+    a protocol used when creating a {@link PhysicalBioAssay}.
+  */
+  public static final String CLUSTER_GENERATION = "net.sf.basedb.core.KitType.CLUSTER_GENERATION";
+
+  /**
+    Get the system id for the kit subtype that should be used on an item
+    that doesn't have a subtype. This includes {@link Subtypable} items with a
+    null {@link ItemSubtype} and all other non-subtypable items which can be
+    linked to a kit.
+    @param itemType The item type
+    @return The system id of the default kit type or null
+  */
+  public static String getDefaultSystemId(Item itemType)
+  {
+    String defaultId = null;
+    if (itemType == Item.SAMPLE)
+    {
+      defaultId = SAMPLING;
+    }
+    else if (itemType == Item.EXTRACT)
+    {
+      defaultId = EXTRACTION;
+    }
+    return defaultId;
+  }
+
   /**
     Create a new <code>Kit</code> item.

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

@@ -197 +197 @@
   @Override
   @SupportsPushAnnotations
-  @SubtypableRelatedItems({Item.HARDWARE, Item.PROTOCOL, Item.EXTRACT})
+  @SubtypableRelatedItems({Item.HARDWARE, Item.PROTOCOL, Item.KIT, Item.EXTRACT})
   public ItemSubtype getItemSubtype()
   {

trunk/www/views/physicalbioassays/bioassays.js

@@ -56 +56 @@
       Buttons.addClickHandler('hardware_id.select', bioassays.selectHardware);
       Events.addEventHandler('hardware_id', 'base-selected', bioassays.setHardwareCallback);
+
+      // Kit
+      Buttons.addClickHandler('kit_id.select', bioassays.selectKit);
+      Events.addEventHandler('kit_id', 'base-selected', bioassays.setKitCallback);
       
       // Array slide
@@ -238 +242 @@
   }
   
+  bioassays.selectKit = function()
+  {
+    var frm = document.forms['bioassay'];
+    var url = '&resetTemporary=1';
+    url += '&tmpfilter:BOOLEAN:inactive=0';
+    url += ItemSubtype.createRelatedFilter('subtype_id', 'KIT');
+    if (frm.kit_id.length > 1) 
+    {
+      var id = Math.abs(parseInt(frm.kit_id[1].value));       
+      url += '&item_id='+id;
+    }
+    Dialogs.selectItem('KIT', 'kit_id', 0, url);
+  }
+  
+  bioassays.setKitCallback = function(event)
+  {
+    var frm = document.forms['bioassay'];
+    var list = frm.kit_id;
+    if (list.length < 2 || list[1].value == '0')
+    {
+      Forms.addListOption(list, 1, new Option());
+    }
+    list[1].value = event.detail.id;
+    list[1].text = event.detail.name;
+    list.selectedIndex = 1;
+  }
+
   bioassays.subtypeOnChange = function()
   {

trunk/www/views/physicalbioassays/edit_bioassay.jsp

@@ -38 +38 @@
   import="net.sf.basedb.core.ItemSubtype"
   import="net.sf.basedb.core.ArraySlide"
+  import="net.sf.basedb.core.Kit"
   import="net.sf.basedb.core.Protocol"
   import="net.sf.basedb.core.Project"
@@ -101 +102 @@
   boolean readCurrentHardware = true;
   Hardware currentHardware = null;
+  
+  boolean readCurrentKit = true;
+  Kit currentKit = null;
 
   if (itemId == 0)
@@ -113 +117 @@
     {
       currentHardware = Base.getFirstMatching(dc, Hardware.getQuery(), "name", cc.getPropertyFilter("creationEvent.hardware.name"));
+    }
+    if (cc.getPropertyFilter("creationEvent.kit.name") != null)
+    {
+      currentKit = Base.getFirstMatching(dc, Kit.getQuery(), "name", cc.getPropertyFilter("creationEvent.kit.name"));
     }
     if (cc.getPropertyFilter("arraySlide.name") != null)
@@ -213 +221 @@
       readCurrentHardware = false;
     }
+    try
+    {
+      currentKit = creationEvent.getKit();
+    }
+    catch (PermissionDeniedException ex)
+    {
+      readCurrentKit = false;
+    }
     
     // Query to retrieve source extracts
@@ -237 +253 @@
   List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL, currentSubtype);
   List<Hardware> recentHardware = (List<Hardware>)cc.getRecent(dc, Item.HARDWARE, currentSubtype);
+  List<Kit> recentKits = (List<Kit>)cc.getRecent(dc, Item.KIT, currentSubtype);
   
   // Query to retrieve item types
@@ -391 +408 @@
             recent="<%=recentHardware%>"
             defaultitems="<%=defaultHardware%>"
+            newitem="<%=pba == null%>"
+          />
+        </td>
+        <td></td>
+      </tr>
+      <tr>
+        <th>Kit</th>
+        <td>
+          <base:select 
+            id="kit_id"
+            clazz="selectionlist"
+            required="false"
+            current="<%=currentKit%>"
+            denied="<%=!readCurrentKit%>"
+            recent="<%=recentKits%>"
             newitem="<%=pba == null%>"
           />

trunk/www/views/physicalbioassays/index.jsp

@@ -34 +34 @@
   import="net.sf.basedb.core.BioMaterialEventSource"
   import="net.sf.basedb.core.Extract"
+  import="net.sf.basedb.core.Kit"
   import="net.sf.basedb.core.Protocol"
   import="net.sf.basedb.core.Hardware"
@@ -233 +234 @@
       }
       
+      int kitId = Values.getInt(request.getParameter("kit_id"), -1);
+      if (kitId >= 0) // < 0 = denied or unchanged
+      {
+        Kit kit = kitId == 0 ? null : Kit.getById(dc, kitId);
+        creationEvent.setKit(kit);
+        if (kit != null) cc.setRecent(kit, subtype, maxRecent);
+      }
+      
       // Extracts
       String[] modifiedExtracts = Values.getString(request.getParameter("+EXTRACT")).split(",");

trunk/www/views/physicalbioassays/list_bioassays.jsp

@@ -262 +262 @@
         title="Hardware"
         sortable="true"
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef 
+        id="kit"
+        property="creationEvent.kit.name"
+        datatype="string"
+        title="Kit"
+        sortable="true" 
         filterable="true"
         exportable="true"
@@ -721 +730 @@
                     enablePropertyLink="<%=mode.hasPropertyLink()%>"
                   /></tbl:cell>
+                <tbl:cell column="kit"
+                  ><base:propertyvalue 
+                    item="<%=creationEvent%>" 
+                    property="kit"
+                    enableEditLink="<%=mode.hasEditLink()%>" 
+                    enablePropertyLink="<%=mode.hasPropertyLink()%>"
+                  /></tbl:cell>
                 <tbl:cell column="eventDate" value="<%=creationEvent.getEventDate()%>" />
                 <tbl:cell column="entryDate" value="<%=creationEvent.getEntryDate()%>" />

trunk/www/views/physicalbioassays/view_bioassay.jsp

@@ -274 +274 @@
         <th>Hardware</th>
         <td><base:propertyvalue item="<%=creationEvent%>" property="hardware" /></td>
+      </tr>
+      <tr>
+        <th>Kit</th>
+        <td><base:propertyvalue item="<%=creationEvent%>" property="kit" /></td>
       </tr>
       <tr>