Changeset 6992

Timestamp:

Nov 3, 2015, 8:19:18 AM (7 years ago)

Author:

Nicklas Nordborg

Message:

References #1958: Add Kit item

Kits can now be selected for extracts in the web client.

Subtype relationships has been implemented and the installer creates "Extraction", "Labeling" and "Library preparation" kit types linked to "Extract", "Labeled extract" and "Library" item types.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/Extract.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Install.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/Kit.java (modified) (1 diff)
• www/biomaterials/extracts/edit_extract.jsp (modified) (7 diffs)
• www/biomaterials/extracts/extracts.js (modified) (3 diffs)
• www/biomaterials/extracts/index.jsp (modified) (2 diffs)
• www/biomaterials/extracts/list_extracts.jsp (modified) (2 diffs)
• www/biomaterials/extracts/view_extract.jsp (modified) (1 diff)

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

@@ -156 +156 @@
   @Override
   @SupportsPushAnnotations
-  @SubtypableRelatedItems({Item.PROTOCOL, Item.HARDWARE, Item.TAG, Item.SAMPLE, Item.EXTRACT})
+  @SubtypableRelatedItems({Item.PROTOCOL, Item.KIT, Item.HARDWARE, Item.TAG, Item.SAMPLE, Item.EXTRACT})
   public ItemSubtype getItemSubtype()
   {

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

@@ -456 +456 @@
       ItemSubtypeData labelingProtocol = createItemSubtype(Item.PROTOCOL, Protocol.LABELING, 
           "Labeling", "Protocols used for creating labeled extracts.", protocolFileType);
-      ItemSubtypeData libraryPreparation = createItemSubtype(Item.PROTOCOL, Protocol.LIBRARY_PREPARATION, 
+      ItemSubtypeData libraryPrepProtocol = createItemSubtype(Item.PROTOCOL, Protocol.LIBRARY_PREPARATION, 
           "Library preparation", "Protocols used for library preparation", protocolFileType);
       createItemSubtype(Item.PROTOCOL, Protocol.POOLING, "Pooling", "Protocols used for creating pooled biomaterails.", protocolFileType);
@@ -473 +473 @@
       createItemSubtype(Item.PROTOCOL, Protocol.FEATURE_EXTRACTION, "Feature extraction", "Protocols used for extracting features from microarray images.", protocolFileType);
   
+      // Kit subtypes
+      createItemSubtype(Item.KIT, Kit.EXTRACTION, "Extraction", "Kits used for creating extracts.");
+      ItemSubtypeData labelingKit = createItemSubtype(Item.KIT, Kit.LABELING, 
+          "Labeling", "Kits used for creating labeled extracts.");
+      ItemSubtypeData libraryPrepKit = createItemSubtype(Item.KIT, Kit.LIBRARY_PREPARATION, 
+          "Library preparation", "Kits used for creating libraries.");
+
       // Hardware subtypes
       ItemSubtypeData scanner = createItemSubtype(Item.HARDWARE, Hardware.SCANNER, 
@@ -502 +509 @@
       ItemSubtypeData labeledExtract = createItemSubtype(Item.EXTRACT, Extract.LABELED, 
         "Labeled extract", "A labeled extract is an extract which has been tagged with a label", 
-        labelTag, labelingProtocol);
+        labelTag, labelingProtocol, labelingKit);
       ItemSubtypeData library = createItemSubtype(Item.EXTRACT, Extract.LIBRARY, 
         "Library", "An extract that has been prepared with an adaptor sequence before sequencing", 
-        barcodeTag, libraryPreparation);
+        barcodeTag, libraryPrepProtocol, libraryPrepKit);
       
       // Physical bioassay subtypes
@@ -1698 +1705 @@
       if (subtype != null)
       {
+        if (related != null)
+        {
+          // Add related subtypes that are missing
+          Map<Integer, ItemSubtypeData> allRelated = subtype.getRelatedSubtypes();
+          for (ItemSubtypeData rel : related)
+          {
+            if (!allRelated.containsKey(rel.getItemType()))
+            {
+              allRelated.put(rel.getItemType(), rel);
+            }
+          }
+        }
+
         log.info("createItemSubtype: EXISTS [SYSTEM ID="+systemId+"; name="+name+"]");
         HibernateUtil.commit(tx);

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

@@ -46 +46 @@
   private static final Item TYPE = Item.KIT;
 
+  /**
+    The ID for the extraction kit type, for example a kit
+    used when creating an {@link Extract} from a {@link
+    Sample}.
+  */
+  public static final String EXTRACTION = "net.sf.basedb.core.KitType.EXTRACTION";
+
+  /**
+    The ID for the labeling kit type, for example a kit
+    used when creating a labeled extract from an {@link Extract}.
+  */
+  public static final String LABELING = "net.sf.basedb.core.KitType.LABELING";
+  
+  /**
+    The ID for the library preparation kit type, for example a kit
+    used when creating a library extract from an {@link Extract}.
+  */
+  public static final String LIBRARY_PREPARATION = "net.sf.basedb.core.KitType.LIBRARY_PREPARATION";
+  
   /**
     Create a new <code>Kit</code> item.

trunk/www/biomaterials/extracts/edit_extract.jsp

@@ -40 +40 @@
   import="net.sf.basedb.core.BioPlate"
   import="net.sf.basedb.core.BioWell"
+  import="net.sf.basedb.core.Kit"
   import="net.sf.basedb.core.Protocol"
   import="net.sf.basedb.core.Project"
@@ -102 +103 @@
   boolean readCurrentProtocol = true;
   Protocol currentProtocol = null;
+  boolean readCurrentKit = true;
+  Kit currentKit = null;
   boolean readCurrentTag = true;
   Tag currentTag = null;
@@ -123 +126 @@
       currentProtocol = Base.getFirstMatching(dc, Protocol.getQuery(), "name", cc.getPropertyFilter("creationEvent.protocol.name"));
     }
+    if (cc.getPropertyFilter("creationEvent.kit.name") != null)
+    {
+      currentKit = Base.getFirstMatching(dc, Kit.getQuery(), "name", cc.getPropertyFilter("creationEvent.kit.name"));
+    }
     if (cc.getPropertyFilter("tag.name") != null)
     {
@@ -212 +219 @@
     {
       readCurrentProtocol = false;
+    }
+    
+    try
+    {
+      currentKit = creationEvent.getKit();
+    }
+    catch (PermissionDeniedException ex)
+    {
+      readCurrentKit = false;
     }
   
@@ -272 +288 @@
 
   // Load recently used items
+  List<Kit> recentKits = (List<Kit>)cc.getRecent(dc, Item.KIT, currentSubtype);
   List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL, currentSubtype);
   List<Sample> recentSamples = (List<Sample>)cc.getRecent(dc, Item.SAMPLE);
@@ -324 +341 @@
     <div id="page-data" class="datacontainer"
       data-extraction-protocoltype-id="<%=SystemItems.getId(Protocol.EXTRACTION)%>"
+      data-extraction-kittype-id="<%=SystemItems.getId(Kit.EXTRACTION) %>"
       data-extract-type="<%=Item.EXTRACT.getValue()%>"
       <%
@@ -450 +468 @@
             recent="<%=recentProtocols%>"
             defaultitems="<%=defaultProtocols%>"
+            newitem="<%=extract == null%>"
+            disabled="<%=lockEventProperties%>"
+          />
+        </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="<%=extract == null%>"
             disabled="<%=lockEventProperties%>"

trunk/www/biomaterials/extracts/extracts.js

@@ -53 +53 @@
       Buttons.addClickHandler('protocol_id.select', extracts.selectProtocol);
       Events.addEventHandler('protocol_id', 'base-selected', extracts.setProtocolCallback);
+      // Kit
+      Buttons.addClickHandler('kit_id.select', extracts.selectKit);
+      Events.addEventHandler('kit_id', 'base-selected', extracts.setKitCallback);
       // Subtype
       Events.addEventHandler('subtype_id', 'change', extracts.subtypeOnChange);
@@ -266 +269 @@
     var tagId = Math.abs(parseInt(frm.tag_id.value));
     if (tagId > 0) parents[parents.length] = 'TAG:'+tagId;
+    var kitId = Math.abs(parseInt(frm.kit_id.value));
+    if (kitId > 0) parents[parents.length] = 'KIT:'+kitId;
+    var protocolId = Math.abs(parseInt(frm.protocol_id.value));
+    if (protocolId > 0) parents[parents.length] = 'PROTOCOL:'+protocolId;
     return parents;
   }
@@ -333 +340 @@
   }
 
+  extracts.selectKit = function()
+  {
+    var frm = document.forms['extract'];
+    var url = '&resetTemporary=1';
+    url += ItemSubtype.createRelatedFilter('subtype_id', 'KIT', Data.int('page-data', 'extraction-kittype-id'));
+    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);
+  }
+  
+  extracts.setKitCallback = function(event)
+  {
+    var frm = document.forms['extract'];
+    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;
+  }
+
+  
   extracts.selectBioPlate = function()
   {

trunk/www/biomaterials/extracts/index.jsp

@@ -35 +35 @@
   import="net.sf.basedb.core.BioPlateEventType"
   import="net.sf.basedb.core.BioWell"
+  import="net.sf.basedb.core.Kit"
   import="net.sf.basedb.core.Protocol"
   import="net.sf.basedb.core.Tag"
@@ -262 +263 @@
           if (pt != null) cc.setRecent(pt, subtype, maxRecent);
         }
+        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);
+        }
       }
       

trunk/www/biomaterials/extracts/list_extracts.jsp

@@ -310 +310 @@
       />
       <tbl:columndef 
+        id="kit"
+        property="creationEvent.kit"
+        sortproperty="creationEvent.kit.name"
+        filterproperty="creationEvent.kit.name"
+        exportproperty="creationEvent.kit.name"
+        datatype="string"
+        title="Kit"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef 
         id="eventDate"
         property="creationEvent.eventDate"
@@ -758 +770 @@
                     item="<%=creationEvent%>" 
                     property="protocol"
+                    enableEditLink="<%=mode.hasEditLink()%>" 
+                    enablePropertyLink="<%=mode.hasPropertyLink()%>"
+                  /></tbl:cell>
+                <tbl:cell column="kit"
+                  ><base:propertyvalue 
+                    item="<%=creationEvent%>" 
+                    property="kit"
                     enableEditLink="<%=mode.hasEditLink()%>" 
                     enablePropertyLink="<%=mode.hasPropertyLink()%>"

trunk/www/biomaterials/extracts/view_extract.jsp

@@ -285 +285 @@
           <th>Protocol</th>
           <td><base:propertyvalue item="<%=creationEvent%>" property="protocol"/></td>
+        </tr>
+        <tr>
+          <th>Kit</th>
+          <td><base:propertyvalue item="<%=creationEvent%>" property="kit"/></td>
         </tr>
         <tr>