Changeset 5648

Timestamp:

May 30, 2011, 12:31:51 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1597: Subtypes of items

Added subtype functionality for extracts. Including the web gui and batch importer.

Fixed some minor problems with samples.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/BasicItem.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Extract.java (modified) (2 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/AbstractItemImporter.java (modified) (6 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/ExtractImporter.java (modified) (10 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/LabeledExtractImporter.java (modified) (4 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/SampleImporter.java (modified) (2 diffs)
• src/test/TestItemImporter.java (modified) (2 diffs)
• src/test/net/sf/basedb/test/roles/UserTest.java (modified) (2 diffs)
• www/biomaterials/extracts/edit_extract.jsp (modified) (15 diffs)
• www/biomaterials/extracts/index.jsp (modified) (3 diffs)
• www/biomaterials/extracts/list_extracts.jsp (modified) (4 diffs)
• www/biomaterials/extracts/view_extract.jsp (modified) (1 diff)
• www/biomaterials/samples/edit_sample.jsp (modified) (2 diffs)

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

@@ -284 +284 @@
     for (Integer itemId : HibernateUtil.loadList(Integer.class, query, getSessionControl()))
     {
-      using.add(new ItemProxy(itemId, itemType));
+      if (itemId != null) using.add(new ItemProxy(itemId, itemType));
     }
   }

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

@@ -200 +200 @@
     throws BaseException
   {   
-    return /*countPhysicalBioAssays() > 0 || */ super.isUsed();
+    return super.isUsed();
   }
   /**
     Get all:
     <ul>
-    <li>{@link PhysicalBioassay}:s created from this extract
+    <li>{@link PhysicalBioAssay}:s created from this extract
     <ul>
     @since 2.2
@@ -213 +213 @@
   {
     Set<ItemProxy> using = super.getUsingItems();
-    // TODO
+    org.hibernate.Session session = getDbControl().getHibernateSession();
+    org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+      "GET_SOURCEEVENTS_FOR_BIOMATERIAL", "bme.physicalBioAssay.id");
+      /*
+        SELECT {1}
+        FROM BioMaterialEventData bme
+        JOIN bme.sources src
+        WHERE index(src) = :bioMaterial
+      */
+    query.setEntity("bioMaterial", this.getData());
+    addUsingItems(using, Item.PHYSICALBIOASSAY, query);
     return using;
   }

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

@@ -1471 +1471 @@
     @param dc The DbControl to use for database access
     @param identifier The identifier protocol
-    @param subtype The biosource subtype, or null if the type doesn't matter
+    @param subtype The sample subtype, or null if the type doesn't matter
     @return A sample, or null if no item could be found
     @since 3.0
@@ -1486 +1486 @@
   
   private ItemQuery<Extract> extractQuery;
+  /**
+    Same as {@link #findSample(DbControl, IdMethod, String, ItemSubtype)}
+    with a null subtype.
+  */
+  protected Extract findExtract(DbControl dc, IdMethod idMethod, String identifier)
+  {
+    return findExtract(dc, idMethod, identifier, null);
+  }
+
   /**
     Find an extract with a given identifier. This is a utility method that
@@ -1494 +1503 @@
     Subsequent calls uses the same query. Thus, this method should always be
     called with the same id method object, otherwise the result is undefined.
-    
+    <p>
+    NOTE! If this method is called with a non-null item subtype parameter and 
+    no extract is found the query will be retried without any subtype.
+  
     @param dc The DbControl to use for database access
     @param identifier The identifier protocol
+    @param subtype The extract subtype, or null if the type doesn't matter
     @return An extract, or null if no item could be found
-  */
-  protected Extract findExtract(DbControl dc, IdMethod idMethod, String identifier)
+    @since 3.0
+  */
+  protected Extract findExtract(DbControl dc, IdMethod idMethod, String identifier, ItemSubtype subtype)
   {
     if (identifier == null) return null;
     if (extractQuery == null) 
     {
-      extractQuery = initReferenceQuery(dc, idMethod, Extract.getQuery(), false);
-    }
-    return findReferencedItem(dc, idMethod, extractQuery, identifier, 0, false);
+      extractQuery = initReferenceQuery(dc, idMethod, Extract.getQuery(), true);
+    }
+    return findReferencedItemWithSubtype(dc, idMethod, extractQuery, identifier, subtype, false);
   }
 
@@ -1536 +1550 @@
       );
     }
-    return findReferencedItem(dc, idMethod, labeledExtractQuery, identifier, 0, false);
+    return findReferencedItem(dc, idMethod, labeledExtractQuery, identifier, SystemItems.getId(Extract.LABELED), false);
   }
   
@@ -1978 +1992 @@
     T item = null;
     Item itemType = query.getItemType();
-    String cacheKey = itemType.name() + ":" + identifier + ":" + subtypeId;
-    if (itemCache.containsKey(cacheKey))
-    {
-      item = (T)itemCache.get(cacheKey);
+    String cacheKey1 = itemType.name() + ":" + identifier;
+    String cacheKey2 = cacheKey1 + ":" + subtypeId;
+    if (itemCache.containsKey(cacheKey2))
+    {
+      item = (T)itemCache.get(cacheKey2);
+    }
+    else if (itemCache.containsKey(cacheKey1))
+    {
+      item = (T)itemCache.get(cacheKey1);
     }
     else
@@ -2025 +2044 @@
           item = accessibleItems.get(0);
         }
-        itemCache.put(cacheKey, item);
+        itemCache.put(cacheKey2, item);
       }
     }

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

@@ -38 +38 @@
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.SystemItems;
+import net.sf.basedb.core.Tag;
 import net.sf.basedb.core.plugin.GuiContext;
 import net.sf.basedb.util.Values;
@@ -57 +58 @@
   private static final Set<GuiContext> guiContexts =  
     Collections.singleton(new GuiContext(Item.EXTRACT, GuiContext.Type.LIST));
-  
+
+  protected static final PluginParameter<String> tagColumnMapping = new PluginParameter<String>(
+      "tagColumnMapping",
+      "Tag",
+      "Mapping that picks the name or ID of a tag from the data columns. The plug-in will first " +
+      "try to find a tag with the given name. If none is found and the value is numeric it will " +
+      "try to load by internal ID. " +
+      "Example: \\Tag\\",
+      optionalColumnMapping
+      );
+
   public ExtractImporter()
   {}
@@ -80 +91 @@
   private Mapper descriptionMapper;
   private Mapper externalIdMapper;
+  private Mapper tagMapper;
   private Mapper originalQuantityMapper;
   private Mapper createdMapper;
@@ -106 +118 @@
   }
   
+  @Override
+  protected Item getItemForSubtypes()
+  {
+    return Item.EXTRACT;
+  }
+
   /**
     Adds column mappings for name, externalId, description,
@@ -116 +134 @@
     parameters.add(internalIdColumnMapping);
     parameters.add(nameColumnMapping);
+    parameters.add(subtypeColumnMapping);
     parameters.add(externalIdColumnMapping);
+    parameters.add(tagColumnMapping);
     parameters.add(descriptionColumnMapping);
     parameters.add(protocolColumnMapping);
@@ -149 +169 @@
     externalIdMapper = getMapper(ffp, (String)job.getValue("externalIdColumnMapping"), 
         cropStrings ? Extract.MAX_EXTERNAL_ID_LENGTH : null, null);
+    tagMapper = getMapper(ffp, (String)job.getValue("tagColumnMapping"), null, null);
     originalQuantityMapper = getMapper(ffp, (String)job.getValue("originalQuantityColumnMapping"), null, null);
     createdMapper = getMapper(ffp, (String)job.getValue("createdColumnMapping"), null, null);
@@ -177 +198 @@
     BioMaterialEvent creationEvent = extract.getCreationEvent();
     if (createdMapper != null) creationEvent.setEventDate(parseDate(createdMapper.getValue(data)));
+    updateItemSubtype(dc, extract, data);
     if (pooledMapper != null)
     {
       extract.setPooled(Values.getBoolean(pooledMapper.getValue(data)));
     }
+
+    if (tagMapper != null) 
+    {
+      String nameOrId = tagMapper.getValue(data);
+      ItemSubtype type = ItemSubtype.getRelatedSubtype(dc, extract, Item.TAG, 0);
+      Tag tag = findTag(dc, FallbackIdMethod.NAME_OR_ID, nameOrId, type);
+      if (nameOrId == null || tag != null) extract.setTag(tag);
+    }
+    
     if (protocolMapper != null) 
     {
       String nameOrId = protocolMapper.getValue(data);
-      ItemSubtype type = ItemSubtype.getById(dc, 
+      ItemSubtype type = ItemSubtype.getRelatedSubtype(dc, extract, Item.PROTOCOL, 
           SystemItems.getId(extract.isPooled() ? Protocol.POOLING : Protocol.EXTRACTION));
       Protocol protocol = findProtocol(dc, FallbackIdMethod.NAME_OR_EXTERNALID_OR_ID, nameOrId, type);
@@ -206 +237 @@
       {
         String nameOrId = parentMapper.getValue(data);
-        Sample sample = findSample(dc, FallbackIdMethod.NAME_OR_EXTERNALID_OR_ID, nameOrId);
+        ItemSubtype type = ItemSubtype.getRelatedSubtype(dc, extract, Item.SAMPLE, 0);
+        Sample sample = findSample(dc, FallbackIdMethod.NAME_OR_EXTERNALID_OR_ID, nameOrId, type);
         Float usedQuantity = usedQuantityMapper == null ?
           null : usedQuantityMapper.getFloat(data);
@@ -228 +260 @@
     {
       String nameOrId = parentMapper.getValue(data);
-      Extract parent = findExtract(dc, FallbackIdMethod.NAME_OR_EXTERNALID_OR_ID, nameOrId);
+      ItemSubtype type = ItemSubtype.getRelatedSubtype(dc, extract, Item.EXTRACT, 0);
+      Extract parent = findExtract(dc, FallbackIdMethod.NAME_OR_EXTERNALID_OR_ID, nameOrId, type);
       if (parent != null)
       {
@@ -234 +267 @@
             null : usedQuantityMapper.getFloat(data);
         extract.getCreationEvent().addSource(parent, usedQuantity);
+        // Use same tag as parent if not yet set and not mapped in the file
+        if (tagMapper == null && parent.getTag() != null && extract.getTag() == null)
+        {
+          extract.setTag(parent.getTag());
+        }
       }
     }

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

@@ -148 +148 @@
   
   /**
-    Calls {@link Extract#getQuery()}.
+    Calls {@link Extract#getQuery()} and set a subtype filter for
+    {@link Extract#LABELED}.
   */
   @Override
@@ -187 +188 @@
   protected Extract createItem(DbControl dc, FlatFileParser.Data data)
   {
-    Tag label = null;
-    if (labelMapper != null) 
-    {
-      ItemSubtype labelType = ItemSubtype.getById(dc, SystemItems.getId(Tag.LABEL));
-      label = findTag(dc, FallbackIdMethod.NAME_OR_ID, labelMapper.getValue(data), labelType);
-    }
-    if (label == null)
-    {
-      // If pooled, try to get the label from the first parent
-      if (pooledMapper != null && parentMapper != null && 
-        Values.getBoolean(pooledMapper.getValue(data)))
-      {
-        Extract parent = findLabeledExtract(dc, FallbackIdMethod.NAME_OR_ID, parentMapper.getValue(data));
-        if (parent != null) label = parent.getTag();
-      }
-    }
     Extract e = Extract.getNew(dc);
-    e.setTag(label);
+    e.setItemSubtype(ItemSubtype.getById(dc, SystemItems.getId(Extract.LABELED)));
     updateItem(dc, e, data);
     return e;
@@ -230 +215 @@
       if (nameOrId == null || protocol != null) creationEvent.setProtocol(protocol);
     }
-    if (labelMapper != null && extract.isInDatabase()) 
+    
+    if (labelMapper != null) 
     {
       String nameOrId = labelMapper.getValue(data);
-      if (nameOrId != null)
-      {
-        ItemSubtype labelType = ItemSubtype.getById(dc, SystemItems.getId(Tag.LABEL));
-        Tag label = findTag(dc, FallbackIdMethod.NAME_OR_ID, labelMapper.getValue(data), labelType);
-        extract.setTag(label);
-      }
-    }
+      ItemSubtype labelType = ItemSubtype.getById(dc, SystemItems.getId(Tag.LABEL));
+      Tag label = findTag(dc, FallbackIdMethod.NAME_OR_ID, labelMapper.getValue(data), labelType);
+      if (nameOrId == null || label != null) extract.setTag(label);
+    }
+    
     if (bioPlateMapper != null && bioWellRowMapper != null && bioWellColMapper != null)
     {
@@ -285 +269 @@
             null : usedQuantityMapper.getFloat(data);
         extract.getCreationEvent().addSource(parent, usedQuantity);
+        // Use same tag as parent if not yet set and not mapped in the file
+        if (labelMapper == null && parent.getTag() != null && extract.getTag() == null)
+        {
+          extract.setTag(parent.getTag());
+        }
       }
     }

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

@@ -295 +295 @@
     if (createdMapper != null) creationEvent.setEventDate(parseDate(createdMapper.getValue(data)));
     updateItemSubtype(dc, sample, data);
+    if (pooledMapper != null)
+    {
+      sample.setPooled(Values.getBoolean(pooledMapper.getValue(data)));
+    }
     if (protocolMapper != null) 
     {
@@ -315 +319 @@
       }
     }
-    if (pooledMapper != null)
-    {
-      sample.setPooled(Values.getBoolean(pooledMapper.getValue(data)));
-    }
     if (!sample.isPooled())
     {

trunk/src/test/TestItemImporter.java

@@ -104 +104 @@
     // Import labeled extracts
     int labledExtractFileId = TestFile.test_create("data/test.batchimport.labeledextracts.txt", false, false);
-    int labledExtractImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.LabeledExtractImporter");
+    int labledExtractImporterId  = extractImporterId;
     int labledExtractJobId = test_create_item_import_job(Item.EXTRACT, labledExtractImporterId, labledExtractFileId);
     ok &= TestJob.test_execute(labledExtractJobId, false);
@@ -353 +353 @@
     if (file.getName().contains("labeledextracts"))
     {
-      request.setParameterValue("labelColumnMapping", "\\Label\\");
+      request.setParameterValue("tagColumnMapping", "\\Label\\");
+      request.setParameterValue("subtypeColumnMapping", "Labeled extract");
+      request.setParameterValue("pooledColumnMapping", "1");
     }
     if (itemType == Item.PHYSICALBIOASSAY)

trunk/src/test/net/sf/basedb/test/roles/UserTest.java

@@ -37 +37 @@
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.FileParameterType;
+import net.sf.basedb.core.ItemSubtype;
 import net.sf.basedb.core.PhysicalBioAssay;
 import net.sf.basedb.core.Include;
@@ -411 +412 @@
     
     Extract labeledExtract = Extract.getNew(dc);
+    labeledExtract.setItemSubtype(ItemSubtype.getById(dc, SystemItems.getId(Extract.LABELED)));
     labeledExtract.setName(name);
     labeledExtract.setOriginalQuantity(100.0f);

trunk/www/biomaterials/extracts/edit_extract.jsp

@@ -34 +34 @@
   import="net.sf.basedb.core.Sample"
   import="net.sf.basedb.core.Extract"
+  import="net.sf.basedb.core.ItemSubtype"
+  import="net.sf.basedb.core.Tag"
   import="net.sf.basedb.core.BioMaterialEvent"
   import="net.sf.basedb.core.BioPlate"
@@ -85 +87 @@
   WellCoordinateFormatter columnFormatter = new WellCoordinateFormatter(false);
 
+  boolean readCurrentSubtype = true;
+  int currentSubtypeId = 0;
   boolean readCurrentProtocol = true;
   Protocol currentProtocol = null;
   Protocol defaultProtocol = null;
+  boolean readCurrentTag = true;
+  Tag currentTag = null;
   boolean readCurrentSample = true;
   Sample currentSample = null;
@@ -103 +109 @@
   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();
@@ -125 +132 @@
       currentProtocol = Base.getFirstMatching(dc, Protocol.getQuery(), "name", cc.getPropertyFilter("creationEvent.protocol.name"));
     }
+    if (cc.getPropertyFilter("tag.name") != null)
+    {
+      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 sampleId = Values.getInt(request.getParameter("sample_id"));
     if (sampleId != 0)
@@ -147 +164 @@
   {
     extract = Extract.getById(dc, itemId);
+    extract.checkPermission(Permission.WRITE);
     cc.setObject("item", extract);
     title = "Edit extract -- " + HTML.encodeTags(extract.getName());
@@ -158 +176 @@
     try
     {
+      ItemSubtype subtype = extract.getItemSubtype();
+      if (subtype != null) currentSubtypeId = subtype.getId();
+    }
+    catch (PermissionDeniedException ex)
+    {
+      readCurrentSubtype = false;
+    }
+
+    try
+    {
       currentProtocol = creationEvent.getProtocol();
     }
@@ -165 +193 @@
     }
   
+    try
+    {
+      currentTag = extract.getTag();
+    }
+    catch (PermissionDeniedException ex)
+    {
+      readCurrentTag = false;
+    }
+
     try
     {
@@ -195 +232 @@
   
   }
-  if (extract != null && !extract.hasPermission(Permission.WRITE))
-  {
-    throw new PermissionDeniedException(Permission.WRITE, itemType.toString());
-  }
+  
+  // Query to retrieve item types
+  final ItemQuery<ItemSubtype> subtypesQuery = Base.getSubtypesQuery(itemType);
+  subtypesQuery.include(Include.ALL);
+
   final String clazz = "class=\"text\"";
   final String requiredClazz = "class=\"text required\"";
@@ -209 +247 @@
   %>
   <base:page type="popup" title="<%=title%>">
-  <base:head scripts="tabcontrol.js,annotations.js,linkitems.js" styles="tabcontrol.css">
+  <base:head scripts="tabcontrol.js,annotations.js,linkitems.js,subtypes.js,ajax.js,json2.js" styles="tabcontrol.css">
     <ext:scripts context="<%=jspContext%>" />
     <ext:stylesheets context="<%=jspContext%>" />
@@ -309 +347 @@
     {
       var frm = document.forms['extract'];
-      var url = '../../admin/protocols/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setProtocolCallback';
+      var url = '../../admin/protocols/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
+      url += '&callback=setProtocolCallback&resetTemporary=1';
+      url += ItemSubtype.createRelatedFilter('extract', 'PROTOCOL', <%=SystemItems.getId(Protocol.EXTRACTION)%>);
       if (frm.protocol_id.length > 1) 
       {
@@ -315 +355 @@
         url += '&item_id='+id;
       }
-      url += '&resetTemporary=1&tmpfilter:INT:itemSubtype=<%=SystemItems.getId(Protocol.EXTRACTION)%>';
       Main.openPopup(url, 'SelectProtocol', 1000, 700);
     }
@@ -334 +373 @@
     {
       protocolChanged = true;
+    }
+    function selectTagOnClick()
+    {
+      var frm = document.forms['extract'];
+      var url = '../tags/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
+      url += '&callback=setTagCallback&resetTemporary=1';
+      url += ItemSubtype.createRelatedFilter('extract', 'TAG');
+      if (frm.tag_id.length > 1) 
+      {
+        var id = Math.abs(parseInt(frm.tag_id[1].value));       
+        url += '&item_id='+id;
+      }
+      Main.openPopup(url, 'SelectTag', 1000, 700);
+    }
+    function setTagCallback(id, name)
+    {
+      var frm = document.forms['extract'];
+      var list = frm.tag_id;
+      if (list.length < 2 || list[1].value == '0') // >
+      {
+        Forms.addListOption(list, 1, new Option());
+      }
+      list[1].value = id;
+      list[1].text = name;
+      list.selectedIndex = 1;
     }
     function selectBioPlateOnClick()
@@ -446 +510 @@
         return;
       }
-      var url = '../samples/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setSampleCallback';
+      var url = '../samples/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
+      url += '&callback=setSampleCallback&resetTemporary=1';
+      url += ItemSubtype.createRelatedFilter('extract', 'SAMPLE');
       if (frm.sample_id.length > 1) 
       {
@@ -476 +542 @@
         return;
       }
-      Main.openPopup('index.jsp?ID=<%=ID%>&mode=selectmultiple&callback=addExtractCallback', 'AddExtracts', 1000, 700);
+      var url = 'index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectmultiple';
+      url += '&callback=addExtractCallback&resetTemporary=1';
+      url += ItemSubtype.createRelatedFilter('extract', 'EXTRACT');
+      Main.openPopup(url, 'AddExtracts', 1000, 700);
     }
     
@@ -595 +664 @@
           value="<%=HTML.encodeTags(name)%>" 
           size="40" maxlength="<%=Extract.MAX_NAME_LENGTH%>"></td>
+      </tr>
+      <tr valign="top">
+        <td class="prompt">Type</td>
+        <td colspan="2">
+          <select name="subtype_id"
+            <%=!readCurrentSubtype ? "disabled readonly class=\"disabled selectionlist\"" : "class=\"selectionlist\""%>>
+          <%
+          if (!readCurrentSubtype)
+          {
+            %>
+            <option value="-1">- denied -
+            <%
+          }
+          else
+          {
+            %>
+            <option value="0">-none-
+            <%
+            for (ItemSubtype subtype : subtypesQuery.list(dc))
+            {
+              int id = subtype.getId();
+              if (id != currentSubtypeId && subtype.isRemoved()) continue;
+              %>
+              <option value="<%=id == currentSubtypeId && extract != null ? -id : id%>" 
+                <%=id == currentSubtypeId ? "selected" : ""%>
+                title="<%=HTML.encodeTags(subtype.getDescription()) %>"
+                ><%=HTML.encodeTags(subtype.getName())%>
+              <%
+            }
+          }
+          %>
+          </select>
+        </td>
+      </tr>
+      <tr>
+        <td class="prompt">Tag</td>
+        <td>
+          <base:select 
+            id="tag_id"
+            clazz="selectionlist"
+            required="false"
+            current="<%=currentTag%>"
+            denied="<%=!readCurrentTag%>"
+            recent="<%=recentTags%>"
+            newitem="<%=extract == null%>"
+            onselect="selectTagOnClick()"
+          />
+        </td>
       </tr>
       <tr>

trunk/www/biomaterials/extracts/index.jsp

@@ -35 +35 @@
   import="net.sf.basedb.core.BioWell"
   import="net.sf.basedb.core.Protocol"
+  import="net.sf.basedb.core.Tag"
   import="net.sf.basedb.core.PhysicalBioAssay"
+  import="net.sf.basedb.core.ItemSubtype"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.ItemResultIterator"
@@ -77 +79 @@
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 <%!
-  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,originalQuantity,remainingQuantity,physicalBioAssays,description");
+  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,itemSubtype,originalQuantity,remainingQuantity,physicalBioAssays,description");
   private static final Item itemType = Item.EXTRACT;
   
@@ -243 +245 @@
       }
       
+      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);
+      }
+      
+      int tagId = Values.getInt(request.getParameter("tag_id"), -1);
+      if (tagId >= 0) // < 0 = denied or unchanged
+      {
+        Tag tag = tagId == 0 ? null : Tag.getById(dc, tagId);
+        extract.setTag(tag);
+        if (tag != null) cc.setRecent(tag, maxRecent);
+      }
+
       int biowellId = Values.getInt(request.getParameter("biowell_id"), -1);
       if (biowellId >= 0) // < 0 = denied or unchanged

trunk/www/biomaterials/extracts/list_extracts.jsp

@@ -34 +34 @@
   import="net.sf.basedb.core.BioMaterialEvent"
   import="net.sf.basedb.core.BioWell"
+  import="net.sf.basedb.core.ItemSubtype"
   import="net.sf.basedb.core.AnnotationType"
   import="net.sf.basedb.core.AnnotationSet"
@@ -99 +100 @@
 {
   final ItemQuery<AnnotationType> annotationTypeQuery = Base.getAnnotationTypesQuery(itemType);
+  final ItemQuery<ItemSubtype> subtypesQuery = Base.getSubtypesQuery(itemType);
   final boolean createBioAssayPermission = sc.hasPermission(Permission.CREATE, Item.PHYSICALBIOASSAY);
 
@@ -291 +293 @@
         exportable="true"
         show="always" 
+      />
+      <tbl:columndef 
+        id="itemSubtype"
+        property="itemSubtype"
+        sortproperty="itemSubtype.name"
+        exportproperty="itemSubtype.name"
+        datatype="int"
+        enumeration="<%=Enumeration.fromItems(subtypesQuery.list(dc), "-none-")%>"
+        title="Type"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
       />
       <tbl:columndef
@@ -704 +718 @@
                   title="<%=tooltip%>"><%=name%></div></tbl:cell>
                 <tbl:cell column="id"><%=item.getId()%></tbl:cell>
+                <tbl:cell column="itemSubtype"><base:propertyvalue 
+                    item="<%=item%>" 
+                    property="itemSubtype"
+                    enableEditLink="<%=mode.hasEditLink()%>" 
+                    enablePropertyLink="<%=mode.hasPropertyLink()%>"
+                  /></tbl:cell>
                 <tbl:cell column="externalId"><%=HTML.encodeTags(item.getExternalId())%></tbl:cell>
                 <tbl:cell column="originalQuantity"><%=Values.formatNumber(item.getOriginalQuantity(), 2)%></tbl:cell>

trunk/www/biomaterials/extracts/view_extract.jsp

@@ -296 +296 @@
       </tr>
       <tr>
+        <td class="prompt">Type</td>
+        <td><base:propertyvalue item="<%=extract%>" property="itemSubtype" /></td>
+      </tr>
+      <tr>
         <td class="prompt">External ID</td>
         <td><%=HTML.encodeTags(extract.getExternalId())%></td>

trunk/www/biomaterials/samples/edit_sample.jsp

@@ -340 +340 @@
         url += '&item_id='+id;
       }
-      url += '&resetTemporary=1&tmpfilter:INT:itemSubtype=<%=SystemItems.getId(Protocol.SAMPLING)%>';
       Main.openPopup(url, 'SelectProtocol', 1000, 700);
     }
@@ -473 +472 @@
       var url = '../biosources/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
       url += '&callback=setBioSourceCallback&resetTemporary=1';
-      ItemSubtype.createRelatedFilter('sample', 'BIOSOURCE');
+      url += ItemSubtype.createRelatedFilter('sample', 'BIOSOURCE');
       if (frm.biosource_id.length > 1) 
       {