Changeset 6947

Timestamp:

Sep 8, 2015, 2:30:31 PM (8 years ago)

Author:

Nicklas Nordborg

Message:

References #1941: Store experimental factor values as part experiments

Implemented support for inheriting new annotations via the "Inherit" button. The 'Inherited annotations' tab has been removed from all dialogs.

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/AnnotationUtil.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (3 diffs)
• www/biomaterials/extracts/edit_extract.jsp (modified) (1 diff)
• www/biomaterials/extracts/extracts.js (modified) (3 diffs)
• www/biomaterials/samples/edit_sample.jsp (modified) (1 diff)
• www/biomaterials/samples/samples.js (modified) (3 diffs)
• www/common/annotations/ajax.jsp (modified) (3 diffs)
• www/common/annotations/annotate.js (modified) (9 diffs)
• www/common/annotations/annotate.jsp (modified) (9 diffs)
• www/common/annotations/batch_inherit.js (modified) (1 diff)
• www/common/annotations/inherit.js (modified) (4 diffs)
• www/common/annotations/inherit.jsp (modified) (7 diffs)
• www/common/annotations/inherit_frameset.jsp (deleted)
• www/include/scripts/annotations.js (modified) (3 diffs)
• www/lims/arraybatches/batches.js (modified) (3 diffs)
• www/lims/arraybatches/edit_batch.jsp (modified) (1 diff)
• www/lims/arraydesigns/designs.js (modified) (2 diffs)
• www/lims/arraydesigns/edit_design.jsp (modified) (1 diff)
• www/lims/arrayslides/edit_slide.jsp (modified) (1 diff)
• www/lims/arrayslides/slides.js (modified) (2 diffs)
• www/lims/plates/edit_plate.jsp (modified) (1 diff)
• www/lims/plates/plates.js (modified) (2 diffs)
• www/lims/plates/wells/edit_well.jsp (modified) (1 diff)
• www/lims/plates/wells/wells.js (modified) (2 diffs)
• www/views/derivedbioassays/bioassays.js (modified) (3 diffs)
• www/views/derivedbioassays/edit_bioassay.jsp (modified) (1 diff)
• www/views/experiments/bioassays/bioassays.js (modified) (2 diffs)
• www/views/experiments/bioassays/edit_bioassay.jsp (modified) (1 diff)
• www/views/experiments/bioassaysets/bioassaysets.js (modified) (2 diffs)
• www/views/experiments/bioassaysets/edit_bioassayset.jsp (modified) (1 diff)
• www/views/experiments/rootrawbioassays/bioassays.js (modified) (2 diffs)
• www/views/experiments/rootrawbioassays/edit_bioassay.jsp (modified) (1 diff)
• www/views/physicalbioassays/bioassays.js (modified) (3 diffs)
• www/views/physicalbioassays/edit_bioassay.jsp (modified) (1 diff)
• www/views/rawbioassays/bioassays.js (modified) (3 diffs)
• www/views/rawbioassays/edit_rawbioassay.jsp (modified) (1 diff)

trunk/src/clients/web/net/sf/basedb/clients/web/AnnotationUtil.java

@@ -22 +22 @@
 package net.sf.basedb.clients.web;
 
+import java.util.ArrayList;
+import java.util.Date;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
 
+import net.sf.basedb.clients.web.formatter.FormatterFactory;
+import net.sf.basedb.clients.web.util.HTML;
+import net.sf.basedb.core.Annotatable;
+import net.sf.basedb.core.Annotation;
 import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.AnnotationTypeCategory;
@@ -33 +40 @@
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.ItemSubtype;
+import net.sf.basedb.core.Nameable;
 import net.sf.basedb.core.Type;
+import net.sf.basedb.core.Unit;
 import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.core.query.Restrictions;
+import net.sf.basedb.util.formatter.Formatter;
 
 import org.json.simple.JSONArray;
@@ -148 +158 @@
   }
   
+  
+  @SuppressWarnings("unchecked")
+  public static JSONObject createJsonForAnnotationTypeAndAnnotation(DbControl dc, AnnotationType at, 
+    Annotation a, Annotation inherited, boolean isProtocolParameter, Set<AnnotationTypeCategory> allCategories)
+  {
+    // Create the JSON objects for holding all info
+    // The base object has 'id', 'source', 'annotationType' and 'annotation'
+    JSONObject json = new JSONObject();
+    json.put("id", ""+at.getId() + (a!=null ? "-" + a.getId() : ""));
+    // If 'a' is null this is a primary annotation that has no current values
+    json.put("source", a == null ? (inherited == null ? "PRIMARY" : "INHERITED") : a.getSource().name());
+
+    JSONObject jsonAt = new JSONObject();
+    json.put("annotationType", jsonAt);
+    JSONObject jsonA = new JSONObject();
+    json.put("annotation", jsonA);
+    JSONArray jsonValues = new JSONArray();
+    jsonA.put("values", jsonValues);
+
+    // Load annotation type information
+    Type valueType = at.getValueType();
+    Formatter formatter = FormatterFactory.getTypeFormatter(dc.getSessionControl(), valueType);
+    
+    jsonAt.put("id", at.getId());
+    jsonAt.put("name", at.getName());
+    jsonAt.put("valueType", valueType.name());
+    jsonAt.put("multiplicity", at.getMultiplicity());
+    jsonAt.put("description", HTML.encodeTags(at.getDescription()));
+    jsonAt.put("removed", at.isRemoved());
+    jsonAt.put("protocolParameter", isProtocolParameter);
+
+    if (valueType == Type.STRING)
+    {
+      jsonAt.put("maxLength", at.getMaxLength());
+    }
+    else if (valueType == Type.INT || valueType == Type.LONG)
+    {
+      jsonAt.put("minValue", at.getMinValueLong());
+      jsonAt.put("maxValue", at.getMaxValueLong());
+    }
+    else if (valueType == Type.FLOAT || valueType == Type.DOUBLE)
+    {
+      jsonAt.put("minValue", at.getMinValueDouble());
+      jsonAt.put("maxValue", at.getMaxValueDouble());
+    }
+    
+    // Enumeration
+    if (at.isEnumeration())
+    {
+      List<?> values = at.getValues();
+      JSONArray jsonEnum = new JSONArray();
+      for (Object val : values)
+      {
+        jsonEnum.add(formatter.format(val));
+      }
+      jsonAt.put("enumeration", jsonEnum);
+      jsonAt.put("displayAsList", at.getDisplayAsList());
+    }
+    
+    // Units
+    if (at.supportUnits())
+    {
+      Unit defaultUnit = at.getDefaultUnit();
+      jsonAt.put("defaultUnit", defaultUnit.getId());
+      jsonAt.put("defaultSymbol", defaultUnit.getDisplaySymbol());
+      
+      if (!at.isEnumeration())
+      {
+        ItemQuery<Unit> unitQuery = at.getUsableUnits();
+        if (unitQuery.count(dc) == 0)
+        {
+          unitQuery = at.getQuantity().getUnits();
+        }
+        else
+        {
+          unitQuery.reset();
+        }
+        unitQuery.order(Orders.desc(Hql.property("referenceFactor")));
+        unitQuery.order(Orders.asc(Hql.property("displaySymbol")));
+        List<Unit> units = new ArrayList<Unit>(unitQuery.list(dc));
+        if (!units.contains(defaultUnit)) units.add(defaultUnit);
+        
+        Unit currentUnit = a != null ? a.getUnit() : null;
+        if (currentUnit != null && !units.contains(currentUnit)) units.add(currentUnit);
+        
+        JSONArray jsonUnits = new JSONArray();
+        for (Unit unit : units)
+        {
+          JSONObject jsonUnit = new JSONObject();
+          jsonUnit.put("id", unit.getId());
+          jsonUnit.put("description", HTML.encodeTags(unit.getName() + " - " + unit.getDescription()));
+          jsonUnit.put("symbol", HTML.encodeTags(unit.getDisplaySymbol()));
+          jsonUnits.add(jsonUnit);
+        }
+        jsonAt.put("units", jsonUnits);
+      }
+    }
+    
+    // Categories
+    JSONArray jsonCategories = new JSONArray();
+    ItemQuery<AnnotationTypeCategory> categoryQuery = at.getCategories();
+    categoryQuery.include(Include.MINE, Include.OTHERS, Include.SHARED, Include.IN_PROJECT);
+    categoryQuery.join(Hql.innerJoin("annotationTypes", "atp"));
+    categoryQuery.restrict(Restrictions.eq(Hql.alias("atp"), Hql.entity(at)));
+    for (AnnotationTypeCategory category : categoryQuery.list(dc))
+    {
+      if (allCategories != null) allCategories.add(category);
+      jsonCategories.add(category.getId());
+    }
+    jsonAt.put("categories", jsonCategories);
+
+    
+    if (a != null)
+    {
+      createJSON(jsonA, dc, a, formatter, false);
+      
+      if (a.getSource() != Annotation.Source.PRIMARY)
+      {
+        inherited = a.getInheritedFrom();
+      }
+    }
+    
+    if (inherited != null)
+    {
+      JSONObject jsonInherited = new JSONObject();
+      createJSON(jsonInherited, dc, inherited, formatter, true);
+      Annotatable inheritedFrom = inherited.getAnnotationSet().getItem(dc);
+      JSONObject jsonFrom = new JSONObject();
+      jsonFrom.put("id", inheritedFrom.getId());
+      jsonFrom.put("name", ((Nameable)inheritedFrom).getName());
+      jsonFrom.put("type", inheritedFrom.getType().name());
+      jsonInherited.put("from", jsonFrom);
+      json.put("inherited", jsonInherited);
+    }
+
+    return json;
+  }
+
+  @SuppressWarnings("unchecked")
+  static void createJSON(JSONObject json, DbControl dc, Annotation a, Formatter formatter, boolean formatAll)
+  {
+    json.put("id", a.getId());
+    Date lastUpdate = a.getLastUpdate();
+    if (lastUpdate != null) json.put("lastUpdate",  lastUpdate.getTime());
+    
+    Unit currentUnit = a.getUnit();
+    if (currentUnit != null) 
+    {
+      json.put("unit", currentUnit.getId());
+      json.put("unitSymbol", currentUnit.getDisplaySymbol());
+    }
+    
+    // Populate the values array
+    List values = a.getValues(null);
+    if (values != null)
+    {
+      JSONArray jsonValues = new JSONArray();
+      json.put("values", jsonValues);
+      
+      for (Object value : values)
+      {
+        // Dates should be formatted to strings using the current date(time) format
+        if (formatAll || value instanceof Date) 
+        {
+          value = formatter.format(value);
+        }
+        jsonValues.add(value.toString());
+      }
+    }
+    
+  }
+
 }

trunk/src/clients/web/net/sf/basedb/clients/web/Base.java

@@ -1444 +1444 @@
         JSONObject jsonA = (JSONObject)jsonModified.get(entryNo);
         Number annotationId = (Number)jsonA.get("annotationId");
+        Number inheritedId = (Number)jsonA.get("inheritedId");
         Number annotationTypeId = (Number)jsonA.get("annotationTypeId");
         JSONArray jsonValues = (JSONArray)jsonA.get("values");
@@ -1479 +1480 @@
             if ("CONVERTED".equals(modifyType)) continue; // Only converted between types
           }
-          
+        }
+        else if (inheritedId != null)
+        {
+          if (!"DELETE".equals(modifyType))
+          {
+            Annotation inherited = Annotation.getById(dc, inheritedId.intValue());
+            a = newAs.inheritAnnotation(inherited, source == Annotation.Source.CLONED);
+          }
         }
         else if (jsonValues != null && jsonValues.size() > 0)
         {
-          a = newAs.getAnnotation(at);
+          if (!"DELETE".equals(modifyType))
+          {
+            a = newAs.getAnnotation(at);
+          }
         }
         
         if (a == null) continue;
         
-        Type valueType = at.getValueType();
-        Number unitId = (Number)jsonA.get("unitId");
-        Unit unit = unitId == null ? null : Unit.getById(dc, unitId.intValue());
-        if (jsonValues == null || jsonValues.size() == 0)
+        if (jsonValues != null && jsonValues.size() > 0)
         {
-          newAs.removeAnnotation(at);
-        }
-        else
-        {
+          Type valueType = at.getValueType();
+          Number unitId = (Number)jsonA.get("unitId");
+          Unit unit = unitId == null ? null : Unit.getById(dc, unitId.intValue());
+          
           Object[] oValues = new Object[jsonValues.size()];
           Formatter<?> formatter = FormatterFactory.getTypeFormatter(dc.getSessionControl(), valueType);
@@ -1505 +1513 @@
           a.setValues(Arrays.asList(oValues), unit);
         }
-        
-        
       }
       

trunk/www/biomaterials/extracts/edit_extract.jsp

@@ -603 +603 @@
     </t:tab>
     
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>      
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/biomaterials/extracts/extracts.js

@@ -41 +41 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', extracts.loadAnnotationsFrame);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', extracts.loadInheritedAnnotationsFrame);
       TabControl.addTabValidator('settings.info', extracts.validateExtract);
 
@@ -231 +230 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       Link.exportActions('extracts');
       frm.submit();
@@ -246 +244 @@
       protocolId = Math.abs(parseInt(frm.protocol_id.value));       
     }
-    Annotations.autoLoadEditFrame(protocolId, ItemSubtype.getSubtypeId('subtype_id'));
-  }
-
-  extracts.loadInheritedAnnotationsFrame = function()
-  {
-    Annotations.autoLoadInheritFrame(extracts.getParents());
-  }
-
+    Annotations.autoLoadEditFrame(protocolId, ItemSubtype.getSubtypeId('subtype_id'), extracts.getParents());
+  }
   
   extracts.getParents = function()

trunk/www/biomaterials/samples/edit_sample.jsp

@@ -559 +559 @@
     </t:tab>
     
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/biomaterials/samples/samples.js

@@ -41 +41 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', samples.loadAnnotationsFrame);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', samples.loadInheritedAnnotationsFrame);
       TabControl.addTabValidator('settings.info', samples.validateSample);
 
@@ -205 +204 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       Link.exportActions('samples');
       frm.submit();
@@ -294 +292 @@
       protocolId = Math.abs(parseInt(frm.protocol_id.value));       
     }
-    Annotations.autoLoadEditFrame(protocolId, ItemSubtype.getSubtypeId('subtype_id'));
-  }
-
-  samples.loadInheritedAnnotationsFrame = function()
-  {
-    Annotations.autoLoadInheritFrame(samples.getParents());
+    Annotations.autoLoadEditFrame(protocolId, ItemSubtype.getSubtypeId('subtype_id'), samples.getParents());
   }
   

trunk/www/common/annotations/ajax.jsp

@@ -25 +25 @@
   import="net.sf.basedb.core.DbControl"
   import="net.sf.basedb.core.AnnotationType"
+  import="net.sf.basedb.core.Annotation"
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.Type"
@@ -34 +35 @@
   import="org.json.simple.JSONObject"
   import="org.json.simple.JSONArray"
+  import="java.util.HashSet"
 %>
 <%
@@ -53 +55 @@
     AnnotationType at = AnnotationType.getById(dc, itemId);
     json.put("annotationType", AnnotationUtil.loadJsonForBatchInherit(dc, at));
+  }
+  else if ("GetAnnotationInfoForInherit".equals(cmd))
+  {
+    dc = sc.newDbControl();
+    Annotation a = Annotation.getById(dc, itemId);
+    AnnotationType at = a.getAnnotationType();
+    JSONObject jsonInfo = AnnotationUtil.createJsonForAnnotationTypeAndAnnotation(dc, at, null, a, false, new HashSet());
+    json.put("info", jsonInfo);
   }
   else

trunk/www/common/annotations/annotate.js

@@ -31 +31 @@
   var CONVERTED = 'CONVERTED';
   var DELETE = 'DELETE';
+  var INHERITED = 'INHERITED';
   
   var annotations;
+  var parents;
   var selectedAnnotation;
   var selectedIndex;
@@ -45 +47 @@
     // Parse the current annotation information which contain value type, current values, etc.
     annotations = Data.json('page-data', 'annotations');
+    parents = Data.json('page-data', 'parents');
+    
     // Loop through all annotations and build the selection list
     var numPrimary = 0;
     for (var i = 0; i < annotations.length; i++)
     {
-      annotate.createAnnotationEntryInList(annotations[i], true);
+      annotate.createAnnotationEntryInList(annotations[i], false);
       if (annotations[i].source == 'PRIMARY') numPrimary++;
     }
@@ -107 +111 @@
     // Delete annotations
     Buttons.addClickHandler('btnDelete', annotate.deleteAllChecked);
+    // Add inherited annotations
+    Buttons.addClickHandler('btnAdd', annotate.addInheritedAnnotations);
+    Events.addEventHandler('btnAdd', 'remove-annotation', annotate.onRemoveInheritedAnnotation);
+    Events.addEventHandler('btnAdd', 'inherit-annotation', annotate.onAddInheritedAnnotation);
     
     // Select the initial annotation
@@ -129 +137 @@
     in the list.
   */
-  annotate.createAnnotationEntryInList = function(entry, firstInherited)
+  annotate.createAnnotationEntryInList = function(entry, autoSort)
   {
     var ann = entry.annotation;
@@ -157 +165 @@
     
     Events.addEventHandler(div, 'click', annotate.annotationOnClick);
-    Doc.element(entry.source == 'PRIMARY' ? 'primary-list' : 'inherited-list').appendChild(div);
+    var list = Doc.element(entry.source == 'PRIMARY' ? 'primary-list' : 'inherited-list');
+    var beforeChild = null;
+    if (autoSort)
+    {
+      var childNo = 0;
+      while (childNo < list.childNodes.length)
+      {
+        var child = list.childNodes[childNo];
+        if (child.title && child.title > div.title)
+        {
+          beforeChild = child;
+          break;
+        }
+        childNo++;
+      }
+    }
+    list.insertBefore(div, beforeChild);
   }
   
@@ -176 +200 @@
 
       var show = false;
-      if (entry.modified == 'DELETE' && entry.source != 'PRIMARY')
-      {} // Do not show deleted annotations that are not PRIMARY
+      if (entry.source != 'PRIMARY')
+      {
+        // INHERITED or CLONED annotations are visible unless DELETEd
+        show = entry.modified != 'DELETE';
+      }
       else if (categoryId == -1)
       {
@@ -871 +898 @@
   annotate.deleteAnnotation = function(entry)
   {
-    App.debug(entry.id);
     if (entry.source == 'PRIMARY')
     {
@@ -885 +911 @@
     }
     return true;
+  }
+  
+  /**
+    Open a popup dialog for selecting parent annotations
+    that should be inherited.
+  */
+  annotate.addInheritedAnnotations = function(event)
+  {
+    var url = 'inherit.jsp?ID='+App.getSessionId();
+    url += '&item_type='+Data.get('page-data', 'item-type');
+    url += '&item_id='+Data.get('page-data', 'item-id');
+    url += '&callback='+event.currentTarget.id;
+    
+    // Items marked for DELETE should show up in the dialog
+    var deleted = [];
+    for (var i = 0; i < annotations.length; i++)
+    {
+      var entry = annotations[i];
+      if (entry.source != 'PRIMARY' && entry.modified == DELETE && entry.annotation.id)
+      {
+        deleted[deleted.length] = entry.annotation.id;
+      }
+    }
+    url += '&deleted='+deleted.join(',');
+    
+    if (parents.length)
+    {
+      url += '&parents='+parents.join('&parents=');
+    }
+    
+    Dialogs.openPopup(url, 'InheritAnnotations', 750, 500);
+  }
+  
+  annotate.setParents = function(newParents)
+  {
+    parents = newParents;
+  }
+  
+  /**
+    Event handler for removing an inherited annotation.
+  */
+  annotate.onRemoveInheritedAnnotation = function(event)
+  {
+    var inheritedId = event.detail.id;
+    for (var i = 0; i < annotations.length; i++)
+    {
+      var entry = annotations[i];
+      if (entry.inherited && entry.inherited.id == inheritedId)
+      {
+        annotate.deleteAnnotation(entry);
+        return;
+      }
+    }
+  }
+  
+  /**
+    Event handler for adding an inherited annotation. Note
+    that the annotation may be an annotation that is already
+    inherited but has been marked for DELETE. In this case the
+    DELETE should be cancelled.
+  */
+  annotate.onAddInheritedAnnotation = function(event)
+  {
+    Doc.show('inherited-list');
+    var inheritedId = event.detail.id;
+    
+    // Check if we have info about this annotation already
+    for (var i = 0; i < annotations.length; i++)
+    {
+      var entry = annotations[i];
+      if (entry.inherited && entry.inherited.id == inheritedId)
+      {
+        entry.modified = INHERITED;
+        Doc.show(entry.id);
+        return;
+      }
+    }
+    
+    // Load info about this annotation
+    var url = 'ajax.jsp?ID='+App.getSessionId();
+    url += '&cmd=GetAnnotationInfoForInherit';
+    url += '&item_id='+inheritedId;
+    
+    var request = Ajax.getXmlHttpRequest();
+    request.open("GET", url, true);
+    request.send(null);
+    Ajax.setReadyStateHandler(request, annotate.inheritInfoLoaded, annotate.inheritInfoLoaded);
+  }
+  
+  /**
+    Callback after we have got information about an annotation
+    that we should inherit.
+  */
+  annotate.inheritInfoLoaded = function(request)
+  {
+    var response = JSON.parse(request.responseText);
+    if (response.status != 'ok')
+    {
+      App.debug(request.responseText);
+      return;
+    }
+    
+    var entry = response.info;
+    entry.modified = INHERITED;
+    
+    annotations[annotations.length] = entry;
+    annotate.createAnnotationEntryInList(entry, true);
   }
   
@@ -1045 +1178 @@
         tmp.source = entry.source;
         tmp.modified = entry.modified;
-        tmp.values = entry.annotation.values;
-        tmp.annotationId = entry.annotation.id;
         tmp.annotationTypeId = entry.annotationType.id;
-        tmp.unitId = entry.annotation.unit;
+        if (entry.annotation)
+        {
+          tmp.values = entry.annotation.values;
+          tmp.annotationId = entry.annotation.id;
+          tmp.unitId = entry.annotation.unit;
+        }
+        if (entry.inherited)
+        {
+          tmp.inheritedId = entry.inherited.id;
+        }
       }
     }

trunk/www/common/annotations/annotate.jsp

@@ -60 +60 @@
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
   import="net.sf.basedb.clients.web.formatter.FormatterSettings"
+  import="net.sf.basedb.clients.web.AnnotationUtil"
   import="net.sf.basedb.util.Values"
   import="org.json.simple.JSONObject"
@@ -75 +76 @@
 <%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
 <%@ taglib prefix="m" uri="/WEB-INF/menu.tld" %>
-<%!
-private JSONObject makeJSON(DbControl dc, AnnotationType at, Annotation a, boolean isProtocolParameter, Set<AnnotationTypeCategory> allCategories)
-{
-  // Create the JSON objects for holding all info
-  // The base object has 'id', 'source', 'annotationType' and 'annotation'
-  JSONObject json = new JSONObject();
-  json.put("id", ""+at.getId() + (a!=null ? "-" + a.getId() : ""));
-  // If 'a' is null this is a primary annotation that has no current values
-  json.put("source", a == null ? "PRIMARY" : a.getSource().name());
-
-  JSONObject jsonAt = new JSONObject();
-  json.put("annotationType", jsonAt);
-  JSONObject jsonA = new JSONObject();
-  json.put("annotation", jsonA);
-  JSONArray jsonValues = new JSONArray();
-  jsonA.put("values", jsonValues);
-
-  // Load annotation type information
-  Type valueType = at.getValueType();
-  Formatter formatter = FormatterFactory.getTypeFormatter(dc.getSessionControl(), valueType);
-  
-  jsonAt.put("id", at.getId());
-  jsonAt.put("name", at.getName());
-  jsonAt.put("valueType", valueType.name());
-  jsonAt.put("multiplicity", at.getMultiplicity());
-  jsonAt.put("description", HTML.encodeTags(at.getDescription()));
-  jsonAt.put("removed", at.isRemoved());
-  jsonAt.put("protocolParameter", isProtocolParameter);
-
-  if (valueType == Type.STRING)
-  {
-    jsonAt.put("maxLength", at.getMaxLength());
-  }
-  else if (valueType == Type.INT || valueType == Type.LONG)
-  {
-    jsonAt.put("minValue", at.getMinValueLong());
-    jsonAt.put("maxValue", at.getMaxValueLong());
-  }
-  else if (valueType == Type.FLOAT || valueType == Type.DOUBLE)
-  {
-    jsonAt.put("minValue", at.getMinValueDouble());
-    jsonAt.put("maxValue", at.getMaxValueDouble());
-  }
-  
-  // Enumeration
-  if (at.isEnumeration())
-  {
-    List<?> values = at.getValues();
-    JSONArray jsonEnum = new JSONArray();
-    for (Object val : values)
-    {
-      jsonEnum.add(formatter.format(val));
-    }
-    jsonAt.put("enumeration", jsonEnum);
-    jsonAt.put("displayAsList", at.getDisplayAsList());
-  }
-  
-  // Units
-  if (at.supportUnits())
-  {
-    Unit defaultUnit = at.getDefaultUnit();
-    jsonAt.put("defaultUnit", defaultUnit.getId());
-    jsonAt.put("defaultSymbol", defaultUnit.getDisplaySymbol());
-    
-    if (!at.isEnumeration())
-    {
-      ItemQuery<Unit> unitQuery = at.getUsableUnits();
-      if (unitQuery.count(dc) == 0)
-      {
-        unitQuery = at.getQuantity().getUnits();
-      }
-      else
-      {
-        unitQuery.reset();
-      }
-      unitQuery.order(Orders.desc(Hql.property("referenceFactor")));
-      unitQuery.order(Orders.asc(Hql.property("displaySymbol")));
-      List<Unit> units = new ArrayList<Unit>(unitQuery.list(dc));
-      if (!units.contains(defaultUnit)) units.add(defaultUnit);
-      
-      Unit currentUnit = a != null ? a.getUnit() : null;
-      if (currentUnit != null && !units.contains(currentUnit)) units.add(currentUnit);
-      
-      JSONArray jsonUnits = new JSONArray();
-      for (Unit unit : units)
-      {
-        JSONObject jsonUnit = new JSONObject();
-        jsonUnit.put("id", unit.getId());
-        jsonUnit.put("description", HTML.encodeTags(unit.getName() + " - " + unit.getDescription()));
-        jsonUnit.put("symbol", HTML.encodeTags(unit.getDisplaySymbol()));
-        jsonUnits.add(jsonUnit);
-      }
-      jsonAt.put("units", jsonUnits);
-    }
-  }
-  
-  // Categories
-  JSONArray jsonCategories = new JSONArray();
-  ItemQuery<AnnotationTypeCategory> categoryQuery = at.getCategories();
-  categoryQuery.include(Include.MINE, Include.OTHERS, Include.SHARED, Include.IN_PROJECT);
-  categoryQuery.join(Hql.innerJoin("annotationTypes", "atp"));
-  categoryQuery.restrict(Restrictions.eq(Hql.alias("atp"), Hql.entity(at)));
-  for (AnnotationTypeCategory category : categoryQuery.list(dc))
-  {
-    allCategories.add(category);
-    jsonCategories.add(category.getId());
-  }
-  jsonAt.put("categories", jsonCategories);
-
-  
-  if (a != null)
-  {
-    createJSON(jsonA, dc, a, formatter, false);
-    
-    if (a.getSource() != Annotation.Source.PRIMARY)
-    {
-      Annotation inherited = a.getInheritedFrom();
-      if (inherited != null)
-      {
-        JSONObject jsonInherited = new JSONObject();
-        createJSON(jsonInherited, dc, inherited, formatter, true);
-        Annotatable inheritedFrom = inherited.getAnnotationSet().getItem(dc);
-        JSONObject jsonFrom = new JSONObject();
-        jsonFrom.put("id", inheritedFrom.getId());
-        jsonFrom.put("name", ((Nameable)inheritedFrom).getName());
-        jsonFrom.put("type", inheritedFrom.getType().name());
-        jsonInherited.put("from", jsonFrom);
-        json.put("inherited", jsonInherited);
-      }
-    }
-
-  }
-
-  return json;
-}
-
-private void createJSON(JSONObject json, DbControl dc, Annotation a, Formatter formatter, boolean formatAll)
-{
-  json.put("id", a.getId());
-  Date lastUpdate = a.getLastUpdate();
-  if (lastUpdate != null) json.put("lastUpdate",  lastUpdate.getTime());
-  
-  Unit currentUnit = a.getUnit();
-  if (currentUnit != null) 
-  {
-    json.put("unit", currentUnit.getId());
-    json.put("unitSymbol", currentUnit.getDisplaySymbol());
-  }
-  
-  // Populate the values array
-  List values = a.getValues(null);
-  if (values != null)
-  {
-    JSONArray jsonValues = new JSONArray();
-    json.put("values", jsonValues);
-    
-    for (Object value : values)
-    {
-      // Dates should be formatted to strings using the current date(time) format
-      if (formatAll || value instanceof Date) 
-      {
-        value = formatter.format(value);
-      }
-      jsonValues.add(value.toString());
-    }
-  }
-  
-}
-
-%>
 <%
 final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
@@ -256 +87 @@
 int annotationTypeId = Values.getInt(request.getParameter("annotationtype_id"));
 final boolean standalone = Values.getBoolean(request.getParameter("standalone"));
+
+// Parent items may have been submitted by caller
+// Each parameter is ITEMTYPE:ID:ID:...
+String[] parents = request.getParameterValues("parents");
 
 final DbControl dc = sc.newDbControl();
@@ -406 +241 @@
     Annotation a = primary.get(at);
     if (at.isRemoved() && a == null) continue;
-    JSONObject json = makeJSON(dc, at, a, protocolParameters.contains(at), allCategories);
+    JSONObject json = AnnotationUtil.createJsonForAnnotationTypeAndAnnotation(dc, at, a, null, protocolParameters.contains(at), allCategories);
     jsonAnnotations.add(json);
   }
@@ -412 +247 @@
   {
     AnnotationType at = a.getAnnotationType();
-    JSONObject json = makeJSON(dc, at, a, false, allCategories);
+    JSONObject json = AnnotationUtil.createJsonForAnnotationTypeAndAnnotation(dc, at, a, null, false, allCategories);
     jsonAnnotations.add(json);
+  }
+  
+  // Build JSON for parents submitted via request parameter
+  JSONArray jsonParents = new JSONArray();
+  if (parents != null)
+  {
+    for (String p : parents) jsonParents.add(p);
+  }
+  boolean canInherit = jsonParents.size() > 0;
+  if (!canInherit && item != null)
+  {
+    Set<Annotatable> parentItems = item.getAnnotatableParents();
+    canInherit = parentItems != null && parentItems.size() > 0;
   }
   %>
@@ -630 +478 @@
     %>
     <div id="page-data" class="datacontainer"
+      data-item-type="<%=itemType.name() %>"
+      data-item-id="<%=itemId %>"
       data-annotations="<%=HTML.encodeTags(jsonAnnotations.toJSONString()) %>"
+      data-parents="<%=HTML.encodeTags(jsonParents.toJSONString()) %>"
       data-annotation-type-id="<%=annotationTypeId%>"
       data-annotation-id="<%=annotationId %>"
@@ -687 +538 @@
         <div id="annotation-list" class="absolutefull parameterlist topborder" 
           style="top: 2em; bottom: 3em;">
-          <tbl:toolbar subclass="bottomborder">
+          <tbl:toolbar subclass="bottomborder" visible="<%=canInherit || annotationTypes.size()>0 || inherited.size()>0 %>">
             <tbl:button id="btnAdd" title="Inherit&hellip;" image="add.png" 
               tooltip="Inherit more annotations..."
+              disabled="<%=!canInherit%>"
             />
             <tbl:button id="btnDelete" title="Delete" image="remove.png" 
@@ -702 +554 @@
               />
           </tbl:toolbar>
-          <div id="primary-list">
-            <div class="first-primary">
-              <base:icon id="check-all-primary" image="check_uncheck.png" subclass="check-all" 
-                tooltip="Toggle all (use CTRL, ALT or SHIFT to check/uncheck)"
-              />
-            </div>
             <%
             if (annotationTypes.size() == 0 && inherited.size() == 0)
@@ -718 +564 @@
             }
             %>
+          <div id="primary-list">
+            <div class="first-primary">
+              <base:icon id="check-all-primary" image="check_uncheck.png" subclass="check-all" 
+                tooltip="Toggle all (use CTRL, ALT or SHIFT to check/uncheck)"
+              />
+            </div>
           </div>
           <div id="inherited-list">

trunk/www/common/annotations/batch_inherit.js

@@ -79 +79 @@
   inherit.annotationTypeInfoLoaded = function(request)
   {
-    App.debug(request.responseText);
     var response = JSON.parse(request.responseText);
     if (response.status != 'ok')

trunk/www/common/annotations/inherit.js

@@ -32 +32 @@
     // Buttons (on standalone dialog)
     Buttons.addClickHandler('close', App.closeWindow);
-    Buttons.addClickHandler('btnSave', inherit.save);
+    Buttons.addClickHandler('btnOk', inherit.save);
     
     Events.addEventHandler('quickFilter', 'keyup', inherit.quickFilter);
@@ -80 +80 @@
   }
   
-  inherit.saveInheritedAnnotationsToForm = function(frm)
+  inherit.saveInheritedAnnotations = function()
   {
     var tree = Doc.element('joust');
+    var target = window.top.opener.document.getElementById(Data.get('page-data', 'callback'));
     
-    var addedAnnotations = [];
-    var removedAnnotations = [];
-    
-    var aFrm = document.forms['annotations'];
+    var frm = document.forms['annotations'];
     var menuElements = tree.getElementsByClassName('joustitem');
     for (var menuNo = 0; menuNo < menuElements.length; menuNo++)
@@ -95 +93 @@
       
       var wasInherited = menuItem.inherited;
-      var isInherited = aFrm[menuItem.id].checked;
+      var isInherited = frm[menuItem.id].checked;
       if (wasInherited != isInherited)
       {
         if (menuItem.type == 'annotation')
         {
+          var detail = {};
+          detail.id = menuItem.externalId;
           if (isInherited) 
           {
-            addedAnnotations[addedAnnotations.length] = menuItem.externalId;
+            Events.sendCustomEvent(target, 'inherit-annotation', detail);
           }
           else
           {
-            removedAnnotations[removedAnnotations.length] = menuItem.externalId;
+            Events.sendCustomEvent(target, 'remove-annotation', detail);  
           }
         }
       }
-    }
-    if (frm.addedAnnotations)
-    {
-      frm.addedAnnotations.value = addedAnnotations.join(',');
-    }
-    else
-    {
-      Forms.addHidden(frm, 'addedAnnotations', addedAnnotations.join(','));
-    }
-    if (frm.removedAnnotations)
-    {
-      frm.removedAnnotations.value = removedAnnotations.join(',');
-    }
-    else
-    {
-      Forms.addHidden(frm, 'removedAnnotations', removedAnnotations.join(','));
     }
   }
@@ -158 +142 @@
   inherit.save = function()
   {
-    var frm = document.forms['modified'];
-    inherit.saveInheritedAnnotationsToForm(frm);
-    frm.submit();
+    inherit.saveInheritedAnnotations();
+    App.closeWindow();
   }
 

trunk/www/common/annotations/inherit.jsp

@@ -124 +124 @@
       HTML.encodeTags(((Nameable)item).getName()) + " <span class=\"itemsubtype\">(" + itemType + ")</span>";
     
-    ItemQuery<Annotation> query = as.getAnnotations();
+    ItemQuery<Annotation> query = as.getAnnotations(Annotation.Source.PRIMARY);
     query.restrict(Restrictions.eq(Hql.property("annotationType.disableInheritance"), Expressions.bool(false)));
     List<Annotation> annotations = query.list(as.getDbControl());
     if (annotations.size() == 0) continue; // With the next AnnotationSet/item
       
-    JSONObject jsonJoust = newJoustEntry(null, icon, input+name, joustId);
-    jsonJoust.put("isOpen", 1);
-    jsonJoust.put("type", "annotation-set");
-    jsonJoust.put("externalId", as.getId());
-    json.add(jsonJoust);
+    JSONObject jsonJoust = null;
 
     SessionControl sc = as.getSessionControl();
@@ -140 +136 @@
       Formatter formatter = FormatterFactory.getAnnotationFormatter(sc, a, null);
       boolean inherited = inheritedAnnotations != null && inheritedAnnotations.contains(a);
+      if (inherited) continue;
+      
+      if (jsonJoust == null)
+      {
+        jsonJoust = newJoustEntry(null, icon, input+name, joustId);
+        jsonJoust.put("isOpen", 1);
+        jsonJoust.put("type", "annotation-set");
+        jsonJoust.put("externalId", as.getId());
+        json.add(jsonJoust);
+      }
+      
       AnnotationType at = a.getAnnotationType();
       String annotationName = at.getName();
@@ -190 +197 @@
 final Item itemType = Item.valueOf(request.getParameter("item_type"));
 final int itemId = Values.getInt(request.getParameter("item_id"));
-final boolean standalone = Values.getBoolean(request.getParameter("standalone"));
+
+//final boolean standalone = Values.getBoolean(request.getParameter("standalone"));
 
 final DbControl dc = sc.newDbControl();
@@ -206 +214 @@
     loadParents(dc, parentAnnotations, parentItems, item);
   }
-  if (standalone)
-  {
-    sc.getCurrentContext(itemType).setObject("item", item); 
-  }
+
   String title = "Inherit annotations to " + 
     HTML.encodeTags((item instanceof Nameable ? ((Nameable)item).getName() : 
@@ -256 +261 @@
       ));
     
+    // Ignore annotations marked for DELETE (so it is possible to re-select them)
+    String d = request.getParameter("deleted");
+    if (d != null)
+    {
+      Integer[] deleted = Values.getInt(d.split(","));
+      if (deleted.length > 0)
+      {
+        inheritedQuery.restrict(Restrictions.not(Restrictions.in(Hql.property("id"), Expressions.parameter("deleted"))));
+        inheritedQuery.setParameter("deleted", java.util.Arrays.asList(deleted), Type.INT);
+      }
+    }
+        
     inheritedQuery.order(Orders.asc(Hql.property("annotationSet")));
     inheritedQuery.order(Orders.asc(Hql.property("annotationType.name")));
@@ -286 +303 @@
   </base:head>
   <base:body>
-    <%
-    if (standalone)
-    {
-      %>
-      <h1><%=title%> <base:help helpid="annotations.inherit" /></h1>
-      <div class="content bottomborder">
-      <%
-    }
-    %>
+    
+  <h1><%=title%> <base:help helpid="annotations.inherit" /></h1>
+  <div class="content bottomborder">
+  
+  <div id="page-data" class="datacontainer"
+    data-callback="<%=HTML.encodeTags(request.getParameter("callback"))%>"
+  ></div>
+  
   <form name="annotations"> 
   <div class="absolutefull">
@@ -352 +368 @@
   </div>
   </form>
-
-    <%
-    if (standalone)
-    {
-      %>
-      </div>
-      <base:buttongroup subclass="dialogbuttons">
-        <base:button id="btnSave" title="Save" />
-        <base:button id="close" title="Cancel" />
-      </base:buttongroup>
-      <form name="modified" method="post" action="index.jsp?ID=<%=ID%>">
-        <input type="hidden" name="cmd" value="SaveAnnotations">
-        <input type="hidden" name="item_type" value="<%=itemType.name()%>">
-        <input type="hidden" name="item_id" value="<%=itemId%>">
-      </form>
-      <%
-    }
-    %>
+  </div>
+
+  <base:buttongroup subclass="dialogbuttons">
+    <base:button id="btnOk" title="Ok" />
+    <base:button id="close" title="Cancel" />
+  </base:buttongroup>
+  
   </base:body>
   </base:page>

trunk/www/include/scripts/annotations.js

@@ -54 +54 @@
     was called. DO NOT USE AS AN EVENT HANDLER.
   */
-  annotations.autoLoadEditFrame = function(protocolId, subtypeId)
+  annotations.autoLoadEditFrame = function(protocolId, subtypeId, parents)
   {
-    if (editFrameLoaded && lastProtocolId == protocolId) return;
-    lastProtocolId = protocolId;
+    if (editFrameLoaded)
+    {
+      if (parents)
+      {
+        frames['annotations'].Annotate.setParents(parents);
+      }
+      return;
+    }
     editFrameLoaded = true;
     
@@ -65 +71 @@
     if (protocolId) url += '&protocol_id='+protocolId;
     if (subtypeId) url += '&subtype_id='+subtypeId;
+    if (parents && parents.length)
+    {
+      for (var i = 0; i < parents.length; i++)
+      {
+        url += '&parents='+parents[i];
+      }
+    }
+
     frames['annotations'].location.replace(url);
   }
@@ -79 +93 @@
   }
   
-  /**
-    Automatically load or reload the 'Inherit annotations' frame. The
-    frame is loaded if it has not previously been loaded, or if
-    the parents parameter has changed since last time this method
-    was called.
-  */
-  annotations.autoLoadInheritFrame = function(parents)
-  {
-    if (inheritFrameLoaded)
-    {
-      if (internal.equalArrays(parents, lastParents)) return;
-    }
-    lastParents = parents;
-    inheritFrameLoaded = true;
-    
-    var url = App.getRoot()+'common/annotations/inherit.jsp?ID='+App.getSessionId();
-    url += '&item_type='+Data.get('annotate-data', 'item-type');
-    url += '&item_id='+Data.get('annotate-data', 'item-id');
-    if (parents && parents.length)
-    {
-      for (var i = 0; i < parents.length; i++)
-      {
-        url += '&parents='+parents[i];
-      }
-    }
-    frames['inheritedAnnotations'].location.replace(url);
-  }
-
-  /**
-    Save all changes to inherited annotations to the given form. If
-    the 'Inherit annotations' frame hasn't been loaded, this
-    call is ignored.
-  */
-  annotations.saveInheritedAnnotationsToForm = function(frm)
-  {
-    if (!inheritFrameLoaded) return;
-    frames['inheritedAnnotations'].Inherit.saveInheritedAnnotationsToForm(frm);
-  }
   
   // Check if two arrays have the same elements

trunk/www/lims/arraybatches/batches.js

@@ -41 +41 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', arrayBatches.loadAnnotationsFrame);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', arrayBatches.loadInheritedAnnotationsFrame);
       TabControl.addTabValidator('settings.info', arrayBatches.validateArrayBatch);
 
@@ -148 +147 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       frm.submit();
     }
@@ -155 +153 @@
   arrayBatches.loadAnnotationsFrame = function()
   {
-    Annotations.autoLoadEditFrame(arrayBatches.getProtocolId());
-  }
-  
-  arrayBatches.loadInheritedAnnotationsFrame = function()
-  {
-    Annotations.autoLoadInheritFrame(arrayBatches.getParents());
+    Annotations.autoLoadEditFrame(arrayBatches.getProtocolId(), null, arrayBatches.getParents());
   }
 

trunk/www/lims/arraybatches/edit_batch.jsp

@@ -280 +280 @@
       </jsp:include>
     </t:tab>
-    
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/lims/arraydesigns/designs.js

@@ -41 +41 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', Annotations.onSwitchToAnnotationsTab);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', Annotations.autoLoadInheritFrame);
       TabControl.addTabActivateListener('settings.datafiles', arrayDesigns.loadDataFilesFrame);
       TabControl.addTabValidator('settings.info', arrayDesigns.validateArrayDesign);
@@ -148 +147 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       DataFiles.writeFileActionsToForm(frm);
       frm.submit();

trunk/www/lims/arraydesigns/edit_design.jsp

@@ -284 +284 @@
       </jsp:include>
     </t:tab>
-    
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/lims/arrayslides/edit_slide.jsp

@@ -206 +206 @@
       </jsp:include>
     </t:tab>
-    
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/lims/arrayslides/slides.js

@@ -40 +40 @@
 
       // Tab validation
-      TabControl.addTabActivateListener('settings.annotations', Annotations.onSwitchToAnnotationsTab);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', arraySlides.loadInheritedAnnotationsFrame);
+      TabControl.addTabActivateListener('settings.annotations', arraySlides.loadAnnotationsFrame);
       TabControl.addTabValidator('settings.info', arraySlides.validateArraySlide);
       
@@ -120 +119 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       frm.submit();
     }
   }
   
-  arraySlides.loadInheritedAnnotationsFrame = function()
+  arraySlides.loadAnnotationsFrame = function()
   {
-    Annotations.autoLoadInheritFrame(arraySlides.getParents());
+    Annotations.autoLoadEditFrame(null, null, arraySlides.getParents());
   }
   

trunk/www/lims/plates/edit_plate.jsp

@@ -211 +211 @@
       </jsp:include>
     </t:tab>
-    
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/lims/plates/plates.js

@@ -41 +41 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', Annotations.onSwitchToAnnotationsTab);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', Annotations.autoLoadInheritFrame);
       TabControl.addTabValidator('settings.info', plates.validatePlate);
 
@@ -131 +130 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       frm.submit();
     }

trunk/www/lims/plates/wells/edit_well.jsp

@@ -119 +119 @@
       </jsp:include>
     </t:tab>
-    
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/lims/plates/wells/wells.js

@@ -41 +41 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', Annotations.onSwitchToAnnotationsTab);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', Annotations.autoLoadInheritFrame);
       TabControl.addTabValidator('settings.info', wells.validateWell);
     }
@@ -112 +111 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       frm.submit();
     }

trunk/www/views/derivedbioassays/bioassays.js

@@ -41 +41 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', bioassays.loadAnnotationsFrame);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', bioassays.loadInheritedAnnotationsFrame);
       TabControl.addTabActivateListener('settings.datafiles', bioassays.loadDataFilesFrame);
       TabControl.addTabValidator('settings.info', bioassays.validateBioAssay);
@@ -182 +181 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       DataFiles.writeFileActionsToForm(frm);
       if (Doc.element('physicalBioAssays')) 
@@ -198 +196 @@
   bioassays.loadAnnotationsFrame = function()
   {
-    Annotations.autoLoadEditFrame(bioassays.getProtocolId(), ItemSubtype.getSubtypeId('subtype_id'));
-  }
-  
-  bioassays.loadInheritedAnnotationsFrame = function()
-  {
-    Annotations.autoLoadInheritFrame(bioassays.getParents());
+    Annotations.autoLoadEditFrame(bioassays.getProtocolId(), ItemSubtype.getSubtypeId('subtype_id'), bioassays.getParents());
   }
 

trunk/www/views/derivedbioassays/edit_bioassay.jsp

@@ -538 +538 @@
       </jsp:include>
     </t:tab>
-    
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/views/experiments/bioassays/bioassays.js

@@ -41 +41 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', Annotations.onSwitchToAnnotationsTab);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', Annotations.autoLoadInheritFrame);
       TabControl.addTabValidator('settings.info', bioassays.validateBioAssay);
     }
@@ -158 +157 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       frm.submit();
     }

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

@@ -109 +109 @@
       </jsp:include>
     </t:tab>
-    
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/views/experiments/bioassaysets/bioassaysets.js

@@ -43 +43 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', Annotations.onSwitchToAnnotationsTab);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', Annotations.autoLoadInheritFrame);
       TabControl.addTabValidator('settings.info', bioassaysets.validateBioAssaySet);
     }
@@ -129 +128 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       frm.submit();
     }

trunk/www/views/experiments/bioassaysets/edit_bioassayset.jsp

@@ -135 +135 @@
       </jsp:include>
     </t:tab>
-    
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/views/experiments/rootrawbioassays/bioassays.js

@@ -41 +41 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', Annotations.onSwitchToAnnotationsTab);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', Annotations.autoLoadInheritFrame);
       TabControl.addTabValidator('settings.info', bioassays.validateBioAssay);
     }
@@ -95 +94 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       frm.submit();
     }

trunk/www/views/experiments/rootrawbioassays/edit_bioassay.jsp

@@ -109 +109 @@
       </jsp:include>
     </t:tab>
-    
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/views/physicalbioassays/bioassays.js

@@ -41 +41 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', bioassays.loadAnnotationsFrame);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', bioassays.loadInheritedAnnotationsFrame);
       TabControl.addTabValidator('settings.info', bioassays.validatePhysicalBioAssay);
       
@@ -174 +173 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       Link.exportActions('extracts');
       frm.submit();
@@ -182 +180 @@
   bioassays.loadAnnotationsFrame = function()
   {
-    Annotations.autoLoadEditFrame(bioassays.getProtocolId(), ItemSubtype.getSubtypeId('subtype_id'));
-  }
-  
-  bioassays.loadInheritedAnnotationsFrame = function()
-  {
-    Annotations.autoLoadInheritFrame(bioassays.getParents());
+    Annotations.autoLoadEditFrame(bioassays.getProtocolId(), ItemSubtype.getSubtypeId('subtype_id'), bioassays.getParents());
   }
   

trunk/www/views/physicalbioassays/edit_bioassay.jsp

@@ -494 +494 @@
       </jsp:include>
     </t:tab>
-    
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/views/rawbioassays/bioassays.js

@@ -41 +41 @@
       // Tab validation
       TabControl.addTabActivateListener('settings.annotations', bioassays.loadAnnotationsFrame);
-      TabControl.addTabActivateListener('settings.inheritedAnnotations', bioassays.loadInheritedAnnotationsFrame);
       TabControl.addTabActivateListener('settings.datafiles', bioassays.loadDataFilesFrame);
       TabControl.addTabValidator('settings.info', bioassays.validateRawBioAssay);
@@ -164 +163 @@
     {
       Annotations.saveModifiedAnnotationsToForm(frm);
-      Annotations.saveInheritedAnnotationsToForm(frm);
       DataFiles.writeFileActionsToForm(frm);
       frm.submit();
@@ -181 +179 @@
   bioassays.loadAnnotationsFrame = function()
   {
-    Annotations.autoLoadEditFrame(bioassays.getProtocolId());
-  }
-  
-  bioassays.loadInheritedAnnotationsFrame = function()
-  {
-    Annotations.autoLoadInheritFrame(bioassays.getParents());
+    Annotations.autoLoadEditFrame(bioassays.getProtocolId(), null, bioassays.getParents());
   }
 

trunk/www/views/rawbioassays/edit_rawbioassay.jsp

@@ -570 +570 @@
       </jsp:include>
     </t:tab>
-    
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" 
-      helpid="annotations.edit.inherited">
-      <jsp:include page="../../common/annotations/inherit_frameset.jsp">
-        <jsp:param name="item_type" value="<%=itemType.name()%>" />
-        <jsp:param name="item_id" value="<%=itemId%>" />
-        <jsp:param name="ID" value="<%=ID%>" />
-      </jsp:include>
-    </t:tab>
     </t:tabcontrol>
     </form>