Changeset 4057

Timestamp:

Dec 13, 2007, 1:45:00 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #771: Make annotations for Bioassays available in bioassay table within a BioassaySet?

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/taglib/table/CellValue.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/AnnotationRestriction.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PropertyFilter.java (modified) (2 diffs)
• www/views/experiments/bioassays/list_bioassays.jsp (modified) (5 diffs)
• www/views/experiments/bioassays/view_bioassay.jsp (modified) (5 diffs)

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/CellValue.java

@@ -23 +23 @@
 */
 package net.sf.basedb.clients.web.taglib.table;
-
-import java.util.List;
 
 import javax.servlet.jsp.JspException;
@@ -97 +95 @@
   */
   private Object value = null;
-  private List<?> list = null;
+  private Iterable<?> list = null;
   private String separator = "; ";
 
@@ -113 +111 @@
   }
   
-  public void setList(List<?> list)
+  public void setList(Iterable<?> list)
   {
     this.list = list;
   }
   
-  public List<?> getList()
+  public Iterable<?> getList()
   {
     return list;
@@ -151 +149 @@
       theSeparator = separator;
     }
-    if (list != null && list.size() > 0)
+    if (list != null)
     {
       for (Object o : list)

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

@@ -191 +191 @@
         
         sqlQuery = HibernateUtil.createSqlQuery(session, sql);
-        sqlQuery.addScalar("annotationset_id", org.hibernate.Hibernate.INTEGER);
+        sqlQuery.addScalar("sid", org.hibernate.Hibernate.INTEGER);
         if (debugSqlEnabled) logSql.debug("Executing annotation query: " + sql);
         List<Integer> ids = HibernateUtil.loadList(Integer.class, sqlQuery, sc);

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

@@ -189 +189 @@
     property before proceeding.
     <p>
-    If the property starts with a # it is a filter on annotations. The rest of
+    If the property starts with a # or ## it is a filter on annotations. The rest of
     the property is the ID of the annotation type, and we use a
-    {@link AnnotationSimpleRestriction} object for the restriction.
+    {@link AnnotationSimpleRestriction} object for the restriction. If there
+    is only one # in the prefix only direct annotations are searched, if there
+    are two ##, inherited annotations are also searched.
     <p>
     If the property starts with a @ the property is a collection of values and
@@ -227 +229 @@
     {
       // Property is id of annotation type: #id
-      int annotationTypeId = (Integer)Type.INT.parseString(property.substring(1));
+      // If prefixed with two ## inherited annotations should be searched
+      boolean searchInherited = property.startsWith("##");
+      int annotationTypeId = (Integer)Type.INT.parseString(property.substring(searchInherited ? 2 : 1));
       restriction = new AnnotationSimpleRestriction(alias, annotationTypeId, getValueType(), 
-        getOperator(), getValueAsObject(), false);
+        getOperator(), getValueAsObject(), searchInherited);
     }
     else

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

@@ -88 +88 @@
 ItemResultIterator<BioAssay> bioAssays = null;
 ItemResultList<AnnotationType> annotationTypes = null;
+ItemResultList<AnnotationType> experimentalFactors = null;
 try
 {
@@ -93 +94 @@
   final BioAssaySet bioAssaySet = BioAssaySet.getById(dc, bioAssaySetId);
   final Experiment experiment = bioAssaySet.getExperiment();
+  final ItemQuery<AnnotationType> experimentalFactorQuery = experiment.getExperimentalFactors();
+  experimentalFactorQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
   final int experimentId = experiment.getId();
   final RawDataType rawDataType = experiment.getRawDataType();
@@ -108 +111 @@
   Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
   annotationTypes = annotationTypeQuery.list(dc);
+  experimentalFactors = experimentalFactorQuery.list(dc);
   try
   {
     final ItemQuery<BioAssay> query = Base.getConfiguredQuery(cc, true, bioAssaySet.getBioAssays(), mode);
+    query.join(Hql.leftJoin("rawParents", "rba"));
     bioAssays = query.iterate(dc);
   }
   catch (Throwable t)
   {
+    t.printStackTrace();
     cc.setMessage(t.getMessage());
   }
   int numListed = 0;
   %>
-  <base:page title="<%=title%>" type="<%=mode.getPageType()%>">
+  <%@page import="net.sf.basedb.util.BioAssaySetUtil"%>
+<base:page title="<%=title%>" type="<%=mode.getPageType()%>">
   <base:head scripts="table.js,tabcontrol.js" styles="table.css,headertabcontrol.css,path.css">
     <script language="JavaScript">
@@ -292 +299 @@
           title="<%=HTML.encodeTags(at.getName())+" [A]"%>" 
           property="<%="#"+at.getId()%>"
+          annotation="true"
+          datatype="<%=at.getValueType().getStringValue()%>"
+          enumeration="<%=annotationEnum%>"
+          sortable="false" 
+          filterable="true" 
+          exportable="true"
+          formatter="<%=formatter%>"
+        />
+        <%
+      }
+      %>
+      <%
+      for (AnnotationType at : experimentalFactors)
+      {
+        Enumeration<String, String> annotationEnum = null;
+        Formatter formatter = FormatterFactory.getTypeFormatter(sc, at.getValueType());
+        if (at.isEnumeration())
+        {
+          annotationEnum = new Enumeration<String, String>();
+          List<?> values = at.getValues();
+          for (Object value : values)
+          {
+            String encoded = formatter.format(value);
+            annotationEnum.add(encoded, encoded);
+          }
+        }
+        %>
+        <tbl:columndef 
+          id="<%="ef"+at.getId()%>"
+          title="<%=HTML.encodeTags(at.getName())+" [EF]"%>" 
+          property="<%="$rba.##"+at.getId()%>"
           annotation="true"
           datatype="<%=at.getValueType().getStringValue()%>"
@@ -484 +522 @@
                   }
                 }
+                for (AnnotationType at : experimentalFactors)
+                {
+                  %>
+                  <tbl:cell column="<%="ef"+at.getId()%>"
+                    ><tbl:cellvalue
+                    list="<%=BioAssaySetUtil.getAnnotationValues(dc, item, at)%>"
+                  /></tbl:cell>
+                  <%
+                }               
                 %>
                 <tbl:cell column="tools">

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

@@ -36 +36 @@
   import="net.sf.basedb.core.BioAssay"
   import="net.sf.basedb.core.RawBioAssay"
+  import="net.sf.basedb.core.Annotatable"
+  import="net.sf.basedb.core.AnnotationSet"
+  import="net.sf.basedb.core.AnnotationType"
+  import="net.sf.basedb.core.Annotation"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.ItemResultList"
@@ -45 +49 @@
   import="net.sf.basedb.core.query.Orders"
   import="net.sf.basedb.core.query.Hql"
+  import="net.sf.basedb.util.formatter.Formatter"
+  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.PermissionUtil"
@@ -50 +56 @@
   import="net.sf.basedb.util.Values"
   import="java.util.Map"
+  import="java.util.List"
+  import="java.util.HashMap"
+  import="java.util.LinkedList"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
@@ -214 +223 @@
           title="Description"
         />
+        <%
+        ItemQuery<AnnotationType> efQuery = experiment.getExperimentalFactors();
+        efQuery.include(Include.ALL);
+        efQuery.order(Orders.asc(Hql.property("name")));
+        ItemResultList<AnnotationType> experimentalFactors = efQuery.list(dc);
+        for (AnnotationType at : experimentalFactors)
+        {
+          Formatter formatter = FormatterFactory.getTypeFormatter(sc, at.getValueType());
+          %>
+          <tbl:columndef
+            id="<%="at"+at.getId()%>"
+            title="<%=HTML.encodeTags(at.getName())%>"
+            formatter="<%=formatter%>"
+          />
+          <%
+        }
+        %>
         <tbl:data>
           <tbl:columns>
@@ -226 +252 @@
               <tbl:cell column="spots"><%=item.getSpots()%></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)
+                  {
+                    List values = a.getValues();
+                    Annotatable aItem = null;
+                    try
+                    {
+                      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 image="edit.gif" 
+                        onclick="<%="editInheritedAnnotation('"+aItem.getType().name()+"',"+aItem.getId()+","+at.getId()+")"%>" 
+                        tooltip="Modify the values of this experimental factor" />
+                      <%
+                    }
+                  }
+                  %>
+                </tbl:cell>
+                <%
+              }
+              %>
             </tbl:row>
             <%