Changeset 6942 for trunk/www/views/experiments/bioassays/view_bioassay.jsp

Timestamp:

Aug 31, 2015, 12:50:45 PM (7 years ago)

Author:

Nicklas Nordborg

Message:

References #1941: Store experimental factor values as part experiments

Updated lists that display experimental factors so that they are able to handle inherited/cloned annotations correctly.

File:

• trunk/www/views/experiments/bioassays/view_bioassay.jsp (modified) (4 diffs)

trunk/www/views/experiments/bioassays/view_bioassay.jsp

@@ -35 +35 @@
   import="net.sf.basedb.core.RawBioAssay"
   import="net.sf.basedb.core.RootRawBioAssay"
+  import="net.sf.basedb.core.Unit"
   import="net.sf.basedb.core.Annotatable"
   import="net.sf.basedb.core.AnnotationSet"
@@ -48 +49 @@
   import="net.sf.basedb.core.query.Orders"
   import="net.sf.basedb.core.query.Hql"
+  import="net.sf.basedb.core.snapshot.SnapshotManager"
+  import="net.sf.basedb.core.snapshot.AnnotationSetSnapshot"
+  import="net.sf.basedb.core.snapshot.AnnotationSnapshot"
+  import="net.sf.basedb.core.snapshot.AnnotationTypeFilter"
   import="net.sf.basedb.util.formatter.Formatter"
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
@@ -202 +207 @@
       <base:section
         id="rawBioAssaySection"
-        title="<%="Raw bioassays (" + rawBioAssays.size() + ")"%>"
+        title="<%="Root raw bioassays (" + rawBioAssays.size() + ")"%>"
         context="<%=cc%>"
         >
@@ -259 +264 @@
               <tbl:rows>
               <%
+              SnapshotManager manager = new SnapshotManager();
+              AnnotationTypeFilter annotationTypeFilter = new AnnotationTypeFilter();
               for (RootRawBioAssay item : rawBioAssays)
               {
                 RawBioAssay rba = item.getRawBioAssay();
+                AnnotationSet as = item.isAnnotated() ? item.getAnnotationSet() : null;
+                AnnotationSetSnapshot snapshot = as == null ? null : manager.getSnapshot(dc, as.getId());
                 %>
                 <tbl:row>
-                  <tbl:cell column="name"><%=Base.getLinkedName(ID, rba, false, true)%></tbl:cell>
+                  <tbl:cell column="name"><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
                   <tbl:cell column="spots"><%=rba.getSpots()%></tbl:cell>
-                  <tbl:cell column="description"><%=HTML.encodeTags(rba.getDescription())%></tbl:cell>
+                  <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
                   <%
-                  AnnotationSet as = item.isAnnotated() ? item.getAnnotationSet() : null;
                   for (AnnotationType at : experimentalFactors)
                   {
-                    String value = "<i>- none -</i>";
-                    List<Annotation> all = as == null ? null : as.findAnnotations(dc, at, true);
-                    Map<Annotatable, List> factorValues = new HashMap<Annotatable, List>();
-                    if (all != null && all.size() > 0)
-                    {
-                      for (Annotation a : all)
+                    Unit unit = at.getDefaultUnit();
+                    String unitSymbol = unit == null ? "" : "&nbsp;" + unit.getDisplaySymbol();
+                    
+                    annotationTypeFilter.setAnnotationType(at);
+                    List<AnnotationSnapshot> all = snapshot == null ? 
+                        null : manager.findAnnotations(dc, snapshot, annotationTypeFilter, true);
+                    %>
+                    <tbl:cell column="<%="at"+at.getId()%>">
+                      <%
+                      if (all != null && all.size() > 0)
                       {
-                        List values = a.getValues();
-                        Annotatable aItem = null;
-                        try
+                        for (AnnotationSnapshot a : all)
                         {
-                          aItem = a.getAnnotationSet().getItem();
-                        }
-                        catch (Throwable t)
-                        {}
-                        List toAdd = factorValues.get(aItem);
-                        if (toAdd == null)
-                        {
-                          toAdd = new LinkedList();
-                          factorValues.put(aItem, toAdd);
-                        }
-                        toAdd.addAll(values);
-                      }
-                    }
-                    %>
-                    <tbl:cell column="<%="at"+at.getId()%>"
-                      >
-                      <%
-                      for (Map.Entry<Annotatable, List> entry : factorValues.entrySet())
-                      {
-                        Annotatable aItem = entry.getKey();
-                        List values = entry.getValue();
-                        %>
-                        <tbl:cellvalue list="<%=values%>" />
-                        <%
-                        if (aItem != null && aItem.hasPermission(Permission.WRITE))
-                        {
-                          %>: <base:icon 
-                              subclass="link auto-init"
-                              data-auto-init="edit-experimental-factor"
-                              data-item-type="<%=aItem.getType().name()%>"
-                              data-item-id="<%=aItem.getId()%>"
-                              data-annotation-type="<%=at.getId()%>"
-                              image="edit.png" 
-                              tooltip="Modify the values of this experimental factor" 
-                            />
+                          List values = a.getActualValues();
+                          %>
+                          <tbl:cellvalue list="<%=values%>" suffix="<%=unitSymbol%>"/>
+                          <base:icon 
+                            subclass="link auto-init"
+                            data-auto-init="edit-experimental-factor"
+                            data-item-type="<%=a.getThisItemType().name()%>"
+                            data-item-id="<%=a.getThisItemId() %>"
+                            data-annotation-type="<%=at.getId() %>"
+                            data-annotation="<%=a.getThisAnnotationId()%>"
+                            visible="<%=writePermission%>"
+                            image="edit.png" 
+                            tooltip="Modify the values of this experimental factor"
+                          />
                           <%
                         }