Changeset 4559

Timestamp:

Oct 3, 2008, 4:23:49 PM (15 years ago)

Author:

Martin Svensson

Message:

Fixes #1092 Add listing of child items that are the same type as the parent

Location:

trunk

Files:

• src/core/net/sf/basedb/core/MeasuredBioMaterial.java (modified) (2 diffs)
• src/test/TestExtract.java (modified) (2 diffs)
• src/test/TestLabeledExtract.java (modified) (2 diffs)
• src/test/TestSample.java (modified) (2 diffs)
• www/biomaterials/extracts/view_extract.jsp (modified) (4 diffs)
• www/biomaterials/labeledextracts/view_labeledextract.jsp (modified) (3 diffs)
• www/biomaterials/samples/view_sample.jsp (modified) (4 diffs)

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

@@ -27 +27 @@
 
 import net.sf.basedb.core.data.MeasuredBioMaterialData;
+import net.sf.basedb.core.query.Expressions;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Restrictions;
 
 /**
@@ -292 +295 @@
     return BioMaterialEvent.getQuery(this);
   }
+  
+  /**
+    Get a query that returns all events where this biomaterial
+    has been used as a source.
+      @return An {@link ItemQuery} object
+      @since 2.9
+   */
+  public ItemQuery<BioMaterialEvent> getPoolingEvents()
+  {
+    ItemQuery<BioMaterialEvent> query = new ItemQuery<BioMaterialEvent>(BioMaterialEvent.class, null);
+    query.setDistinct(true);  // Otherwise, the join to sources can result in one copy for each source
+    query.joinPermanent(Hql.leftJoin("sources", "src"));
+    query.joinPermanent(Hql.leftJoin("bioMaterial", "bm"));
+    query.restrictPermanent(
+      Restrictions.and(
+        Restrictions.eq(
+          Hql.index("src", null), 
+          Hql.entity(this)
+        ),
+        Restrictions.eq(
+          Hql.property("bm", "pooled"), 
+          Expressions.integer(1)
+        ),
+        Restrictions.eq(
+          Hql.property("eventType"),
+          Expressions.integer(BioMaterialEvent.Type.CREATION.getValue())
+        )
+      )
+    );
+    return query;   
+  }
 }
-

trunk/src/test/TestExtract.java

@@ -60 +60 @@
     test_list_sources(id3, 1); // The sample
     test_list_sources(id4, 3); // The three id, id2 and id3 extracts
+    test_list_pooledChildren(id2, 1);
 
     if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
@@ -401 +402 @@
     }
   }
-
+  static void test_list_pooledChildren(int extractId, int expectedResults)
+  {
+    if (extractId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      Extract e = Extract.getById(dc, extractId);
+      ItemResultList<BioMaterialEvent> ev = e.getPoolingEvents().list(dc);
+      
+      for (int i=0; i<ev.size(); i++)
+      {
+        write_item(i, (Extract)ev.get(i).getBioMaterial());
+      }
+      if (expectedResults >= 0 && expectedResults != ev.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+ev.size());
+      }
+      write("--List pools from extract OK ("+ev.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List pools for extract FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
 }

trunk/src/test/TestLabeledExtract.java

@@ -60 +60 @@
     test_list_sources(id3, 1); // The extract
     test_list_sources(id4, 3); // The three id, id2 and id3 labeled extracts
+    test_list_pooledChildren(id2, 1);
     test_list_hybridizations(id, 0);
 
@@ -440 +441 @@
     }
   }
-
+  
+  static void test_list_pooledChildren(int labeledExtractId, int expectedResults)
+  {
+    if (labeledExtractId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      LabeledExtract le = LabeledExtract.getById(dc, labeledExtractId);
+      ItemResultList<BioMaterialEvent> ev = le.getPoolingEvents().list(dc);
+      
+      for (int i=0; i<ev.size(); i++)
+      {
+        write_item(i, (LabeledExtract)ev.get(i).getBioMaterial());
+      }
+      if (expectedResults >= 0 && expectedResults != ev.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+ev.size());
+      }
+      write("--List pools from labeledExtract OK ("+ev.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List pools for labeled extract FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
 }

trunk/src/test/TestSample.java

@@ -59 +59 @@
     write_sources_header();
     test_list_sources(id4, 3); // The three id, id2 and id3 samples
+    test_list_pooledChildren(id2, 1);
 
     // Standard test: Delete
@@ -400 +401 @@
     }
   }
-
+  static void test_list_pooledChildren(int sampleId, int expectedResults)
+  {
+    if (sampleId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      Sample s = Sample.getById(dc, sampleId);
+      ItemResultList<BioMaterialEvent> ev = s.getPoolingEvents().list(dc);
+      
+      for (int i=0; i<ev.size(); i++)
+      {
+        write_item(i, (Sample)ev.get(i).getBioMaterial());
+      }
+      if (expectedResults >= 0 && expectedResults != ev.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+ev.size());
+      }
+      write("--List pools from sample OK ("+ev.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List pools for sample FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
 }

trunk/www/biomaterials/extracts/view_extract.jsp

@@ -388 +388 @@
 
       // Extracts this item is pooled in.
-      Set<ItemProxy> childSet = extract.getUsingItems();
-      List<Extract> childExtracts = new ArrayList<Extract>();
-      for (ItemProxy itemProxy : childSet)
-      {
-        if (Item.EXTRACT.equals(itemProxy.getType()))
-        {
-          childExtracts.add((Extract)itemProxy.getItem(dc));
-        }
-      }
-      if (childExtracts.size() == 0)
+      ItemQuery<BioMaterialEvent> poolingQuery = extract.getPoolingEvents();
+      ItemResultList<BioMaterialEvent> poolingEvents = poolingQuery.list(dc);
+      if (poolingEvents.size() == 0)
       {
         %>
@@ -434 +427 @@
             <tbl:rows>
             <%
-            for (Extract e : childExtracts)
+            for (BioMaterialEvent poolEvt : poolingEvents)
             {
-              BioMaterialEvent poolEvent = e.getCreationEvent();
-              ItemQuery<Extract> extractsQuery = (ItemQuery<Extract>)poolEvent.getSources();
+              ItemQuery<Extract> extractsQuery = (ItemQuery<Extract>)poolEvt.getSources();
+              Extract child = (Extract)poolEvt.getBioMaterial();
               extractsQuery.include(Include.ALL);
               extractsQuery.order(Orders.asc(Hql.property("name")));
@@ -447 +440 @@
                     image="deleted.gif" 
                     tooltip="This item has been scheduled for deletion" 
-                    visible="<%=e.isRemoved()%>"
+                    visible="<%=child.isRemoved()%>"
                   />
-                  <%=Base.getLinkedName(ID, e, false, true)%>
+                  <%=Base.getLinkedName(ID, child, false, true)%>
                 </tbl:cell>
-                <tbl:cell column="quantity"><%=Values.formatNumber(e.getOriginalQuantity(), 2)%></tbl:cell>
+                <tbl:cell column="quantity"><%=Values.formatNumber(child.getOriginalQuantity(), 2)%></tbl:cell>
                 <tbl:cell column="parents">
                 <%
@@ -462 +455 @@
                   else                    
                     out.write(Base.getLinkedName(ID, parent, false, true));
-                  out.write("[" + Values.formatNumber(poolEvent.getUsedQuantity(parent), 2) + "µg]");
+                  out.write("[" + Values.formatNumber(poolEvt.getUsedQuantity(parent), 2) + "µg]");
                   separator = ", ";
                 }
                 %>
                 </tbl:cell>
-                <tbl:cell column="description"><%=HTML.encodeTags(e.getDescription())%></tbl:cell>
+                <tbl:cell column="description"><%=HTML.encodeTags(child.getDescription())%></tbl:cell>
               </tbl:row>
               <%

trunk/www/biomaterials/labeledextracts/view_labeledextract.jsp

@@ -39 +39 @@
   import="net.sf.basedb.core.Protocol"
   import="net.sf.basedb.core.User"
+  import="net.sf.basedb.core.ItemProxy"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.ItemResultIterator"
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.Include"
+  import="net.sf.basedb.core.MeasuredBioMaterial"
   import="net.sf.basedb.core.MultiPermissions"
   import="net.sf.basedb.core.query.Orders"
@@ -57 +59 @@
   import="net.sf.basedb.util.formatter.Formatter"
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
+  import="java.util.ArrayList"
   import="java.util.Collections"
   import="java.util.Date"
@@ -387 +390 @@
         <%
       }
+      
+      // Pooled item this labeled extract is used in.     
+      ItemQuery<BioMaterialEvent> poolingQuery = extract.getPoolingEvents();
+      ItemResultList<BioMaterialEvent> poolingEvents = poolingQuery.list(dc);
+      if (poolingEvents.size() == 0)
+      {
+        %>
+        <h4>Pooled in labeled extracts</h4>
+        No labeled extracts have been pooled from this labeled extract
+        (or, you don't have permission to view them).
+        <%
+      }
+      else
+      {
+        %>
+        <h4 class="docked">Pooled in labeled extracts</h4>
+        <tbl:table 
+          id="poolChilds"
+          clazz="itemlist"
+          columns="all"
+          >
+          <tbl:columndef 
+            id="name"
+            title="Name"
+          />
+          <tbl:columndef 
+            id="quantity"
+            title="Original quantity (µg)"
+          />
+          <tbl:columndef 
+            id="parents"
+            title="Used labeled extracts [quantity]" 
+          />
+          <tbl:columndef 
+            id="description"
+            title="Description"
+          />
+          <tbl:data>
+            <tbl:columns></tbl:columns>
+            <tbl:rows>
+            <%
+            for (BioMaterialEvent poolEvt : poolingEvents)
+            {
+              LabeledExtract ch = (LabeledExtract)poolEvt.getBioMaterial();
+              ItemQuery<LabeledExtract> extractsQuery = (ItemQuery<LabeledExtract>)poolEvt.getSources();
+              extractsQuery.include(Include.ALL);
+              extractsQuery.order(Orders.asc(Hql.property("name")));
+              ItemResultList<LabeledExtract> parentExtracts = extractsQuery.list(dc);
+              %>
+              <tbl:row>
+                <tbl:cell column="name">
+                  <base:icon 
+                    image="deleted.gif" 
+                    tooltip="This item has been scheduled for deletion" 
+                    visible="<%=ch.isRemoved() %>"
+                  />
+                  <%=Base.getLinkedName(ID, ch, false, true)%>
+                </tbl:cell>
+                <tbl:cell column="quantity"><%=Values.formatNumber(ch.getOriginalQuantity(), 2)%></tbl:cell>
+                <tbl:cell column="parents">
+                <%
+                String separator = "";
+                for (LabeledExtract parent : parentExtracts)
+                {
+                  out.write(separator);
+                  if (parent.equals(extract))
+                      out.write(HTML.encodeTags(parent.getName()));
+                  else                    
+                    out.write(Base.getLinkedName(ID, parent, false, true));
+                  out.write("[" + Values.formatNumber(poolEvt.getUsedQuantity(parent), 2) + "µg]");
+                  separator = ", ";
+                }
+                %>
+                </tbl:cell>
+                <tbl:cell column="description"><%=HTML.encodeTags(ch.getDescription())%></tbl:cell>
+              </tbl:row>
+              <%
+            }
+            %>            
+            </tbl:rows>
+          </tbl:data>
+        </tbl:table>
+        <%
+      }
+      
       ItemQuery<Hybridization> hybridizationQuery = extract.getHybridizations();
       hybridizationQuery.include(Include.ALL);

trunk/www/biomaterials/samples/view_sample.jsp

@@ -373 +373 @@
       
       // Samples this item is pooled in.
-      Set<ItemProxy> childSet = sample.getUsingItems();
-      List<Sample> childSamples = new ArrayList<Sample>();
-      for (ItemProxy itemProxy : childSet)
-      {
-        if (Item.SAMPLE.equals(itemProxy.getType()))
-        {
-          childSamples.add((Sample)itemProxy.getItem(dc));
-        }
-      }
-      if (childSamples.size() == 0)
+      ItemQuery<BioMaterialEvent> poolingQuery = sample.getPoolingEvents();
+      ItemResultList<BioMaterialEvent> poolingEvents = poolingQuery.list(dc);
+      if (poolingEvents.size() == 0)
       {
         %>
@@ -419 +412 @@
             <tbl:rows>
             <%
-            for (Sample s : childSamples)
+            for (BioMaterialEvent poolingEvt : poolingEvents)
             {
-              BioMaterialEvent poolEvent = s.getCreationEvent();
-              ItemQuery<Sample> samplesQuery = (ItemQuery<Sample>)poolEvent.getSources();
+              Sample child = (Sample)poolingEvt.getBioMaterial();
+              ItemQuery<Sample> samplesQuery = (ItemQuery<Sample>)poolingEvt.getSources();
               samplesQuery.include(Include.ALL);
               samplesQuery.order(Orders.asc(Hql.property("name")));
@@ -432 +425 @@
                     image="deleted.gif" 
                     tooltip="This item has been scheduled for deletion" 
-                    visible="<%=s.isRemoved()%>"
+                    visible="<%=child.isRemoved()%>"
                   />
-                  <%=Base.getLinkedName(ID, s, false, true)%>
+                  <%=Base.getLinkedName(ID, child, false, true)%>
                 </tbl:cell>
-                <tbl:cell column="quantity"><%=Values.formatNumber(s.getOriginalQuantity(), 2)%></tbl:cell>
+                <tbl:cell column="quantity"><%=Values.formatNumber(child.getOriginalQuantity(), 2)%></tbl:cell>
                 <tbl:cell column="parents">
                 <%
@@ -447 +440 @@
                   else                    
                     out.write(Base.getLinkedName(ID, parent, false, true));
-                  out.write("[" + Values.formatNumber(poolEvent.getUsedQuantity(parent), 2) + "µg]");
+                  out.write("[" + Values.formatNumber(poolingEvt.getUsedQuantity(parent), 2) + "µg]");
                   separator = ", ";
                 }
                 %>
                 </tbl:cell>
-                <tbl:cell column="description"><%=HTML.encodeTags(s.getDescription())%></tbl:cell>
+                <tbl:cell column="description"><%=HTML.encodeTags(child.getDescription())%></tbl:cell>
               </tbl:row>
               <%