Changeset 3045

Timestamp:

Dec 20, 2006, 3:37:29 PM (17 years ago)

Author:

Nicklas Nordborg

Message:

References #262 and #340. The overview and validation is now complete.
Still missing possibility to save validation options as presets.

Location:

trunk

Files:

• doc/development/drafts/experiment_overview.txt (modified) (15 diffs)
• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Project.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/ExperimentOverview.java (modified) (47 diffs)
• src/core/net/sf/basedb/util/overview/Failure.java (modified) (4 diffs)
• src/core/net/sf/basedb/util/overview/Fix.java (added)
• src/core/net/sf/basedb/util/overview/Validator.java (modified) (12 diffs)
• www/common/annotations/inherit.jsp (modified) (4 diffs)
• www/filemanager/directories/list_directories.jsp (modified) (1 diff)
• www/filemanager/files/list_files.jsp (modified) (1 diff)
• www/filemanager/frameset.jsp (modified) (1 diff)
• www/filemanager/manager.jsp (modified) (1 diff)
• www/images/configure.png (added)
• www/images/configure_disabled.png (added)
• www/include/scripts/newjoust.js (modified) (3 diffs)
• www/include/styles/main.css (modified) (1 diff)
• www/include/styles/newjoust.css (modified) (1 diff)
• www/views/experiments/overview/failures.jsp (modified) (3 diffs)
• www/views/experiments/overview/frameset.jsp (modified) (1 diff)
• www/views/experiments/overview/index.jsp (modified) (1 diff)
• www/views/experiments/overview/info.jsp (added)
• www/views/experiments/overview/options.jsp (modified) (5 diffs)
• www/views/experiments/overview/overview.jsp (modified) (5 diffs)
• www/views/experiments/overview/tree.jsp (modified) (5 diffs)

trunk/doc/development/drafts/experiment_overview.txt

@@ -49 +49 @@
 warnings for each node. 
 
+After the first prototype we have found that warnings should be attached to
+the nodes that has the possibility to correct the warning/error. In most cases
+this means that the warnings should be attached to: rawbioassay, scan, hybridization,
+labeled extract, extract, sample, biosource, array slide, array batch and array
+design. One exception is 'Access denied' warnings that can't be corrected by the
+logged in user anyway.
+
+We will also try to add a list of possible "fixes" to a warning. A fix consists
+of an explaining text and an item that should be edited.
+
 If an item can't be reached due to a PermissionDeniedException, it should be 
 displayed as a question mark icon for the item that is linking to it.
@@ -63 +73 @@
 Warnings:
  - the raw data type is not the same as the project default raw data type
+   (possible fix: change project default)
+   (done)
  - the raw bioassays has different array designs
+   (no fix) 
+   (done)
  - if there is more than one item of the same type and name
    (checked against all items in the project)
+   (possible fix: rename the item)
+   (done)
 
  
@@ -86 +102 @@
  - Protocol
  
-Warnnings:
- - the raw data type is not the same as the project default raw data type
+Warnings:
+ - the raw data type is not the same as the project default raw data type 
+   (possible fix: change project default)
+   (done)
  - missing array design
+   (no fix)
+   (done)
  - missing value for experimental factor
+   (possible fix: add value or inherit from parent item)
+   (done)
  - array design is different from array design via hybridization
+   (possible fix: change array slide of hyb)
+   (done)
  - missing scan
- - missing protocol
+   (possible fix: add scan)
+   (done)
+ - missing protocol
+   (possible fix: add protocol)
+   (done)
  - missing software
+   (possible fix: add software)
+   (done)
 
 
@@ -100 +130 @@
 Subnodes: none
 Warnings:
- - not same as the project default 
-
- 
+ - not same as the project default (warning is added to parent item)
+   (possible fix: change project default)
+   (done)
+
 Protocol
 ========
@@ -112 +143 @@
 Warnings:
  - not same as the project default
+   (possible fix: change protocol, change project default)
+   (done)
  - incorrect protocol type
+   (possible fix: change protocol, change protocol type)
+   (done)
  - missing value for a parameter
-
-Note! Protocols are always validated together with the item they are attached to
+   (possible fix: add parameter value)
+   (done)
+
+Note! Protocols are always validated together with the item they are attached 
+to and are added to the parent item
 
 Annotation
@@ -123 +161 @@
 Warnings:
  - invalid annotation value according to annotation type
+   (possible fix: change annotation value)
+   (done)
  - inheriting value from non-parent
+   (possible fix: change inherited annotations)
+   (done)
  - inheriting multiple annotation of the same type (from different parents)
+   (possible fix: change inherited annotations)
+   (done)
  - annotation type is a protocol parameter
+   (possible fix: remove annotation value, remove 'parameter' flag from annotation type)
+   (done)
  - annotation type is not valid for the current item type
+   (possible fix: remove annotation value, add item type to annotation type)
+   (done)
  - missing value for a "Required by MIAME" annotation type (on folder node)
-
-Note! Annotations are always validated together with the item they are attached to
+   (possible fix: add annotation value, uncheck the 'Required by MIAME' flag)
+   (done)
+
+Note! Annotations are always validated together with the item they are attached 
+to and the warnnings are added to that item
 
 Software
 ========
 Subnodes: none
-Warnings:
+Warnings (added to parent item):
  - incorrect software type
+   (possible fix: change software, change software type)
+   (done)
+ - not same as project default
+   (possible fix: change software, change project default)
+   (done)
  
 Hardware
 ========
 Subnodes: none
-Warnings:
+Warnings (added to parent item):
  - incorrect hardware type
+   (possible fix: change hardware, change hardware type)
+   (done)
+ - not same as project default
+   (possible fix: change software, change project default)
+   (done)
  
 Scan
@@ -156 +217 @@
 Warnings:
  - missing scanner
- - missing protocol
+   (possible fix: add scanner)
+   (done)
+ - missing protocol
+   (possible fix: add protocol)
+   (done)
  - missing hybridization
+   (possible fix: add hybridization)
+   (done)
 
 Hybridization
@@ -172 +239 @@
 Warnings:
  - missing hybridization station
- - missing protocol
+   (possible fix: add hyb station)
+   (done)
+ - missing protocol
+   (possible fix: add protocol)
+   (done)
  - missing array slide
+   (possible fix: add array slide)
+   (done)
  - wrong number of labeled extracts (checked against experiment raw data type)
+   (possible fix: add/remove labeled extracts)
+   (done)
  - the labeled extracts doesn't have unique labels
+   (possible fix: add/remove labeled extracts, change label of labeled extract)
+   (done)
  
 Array slide
@@ -199 +276 @@
 Warnings:
  - missing print robot
- - missing protocol
- 
+   (possible fix: add print robot)
+   (done)
+ - missing protocol
+   (possible fix: add protocol)
+   (done)
 
 Labeled extract (non-pooled)
@@ -213 +293 @@
 Warnings:
  - missing protocol
+   (possible fix: add protocol)
+   (done)
  - missing extract
+   (possible fix: add extract)
+   (done)
  
 Labeled extract (pooled)
@@ -226 +310 @@
 Warnings:
  - parents use different label
+   (possible fix: add/remove parents, change label of parents)
+   (done)
  - missing parents
+   (possible fix: add parents)
+   (done)
  - circular reference
+   (possible fix: add/remove parents)
+   (done)
  
 Extract (non-pooled)
@@ -240 +330 @@
 Warnings:
  - missing protocol
+   (possible fix: add protocol)
+   (done)
  - missing sample
+   (possible fix: add sample)
+   (done)
  
 Extract (pooled)
@@ -253 +347 @@
 Warnings:
  - missing protocol
+   (possible fix: add protocol)
+   (done)
+ - missing parents
+   (possible fix: add parents)
+   (done)
  - circular reference
+   (possible fix: add/remove parents)
+   (done)
  
 Sample (non-pooled)
@@ -266 +367 @@
 Warnings:
  - missing protocol
+   (possible fix: add protocol)
+   (done)
  - missing biosource
+   (possible fix: add biosource)
+   (done)
 
 Sample (pooled)
@@ -279 +384 @@
 Warnings:
  - missing protocol
+   (possible fix: add protocol)
+   (done)
+ - missing parents
+   (possible fix: add parents)
+   (done)
  - circular reference
+   (possible fix: add/remove parents)
+   (done)
  
 Biosource

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

@@ -948 +948 @@
         {
           AnnotationType at = AnnotationType.getById(dc, annotationTypeId);
-          Annotation oldAn = oldAs == null ? null : oldAs.getAnnotation(at);
+          Annotation oldAn = oldAs == null || !oldAs.hasAnnotation(at) ? 
+            null : oldAs.getAnnotation(at);
           Annotation newAn = newAs.getAnnotation(at);
           if (oldAn == null && newAn.isInDatabase() || oldAn != null && oldAn.getValuesVersion() != newAn.getValuesVersion())

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

@@ -606 +606 @@
   public enum Default
   {   
-    SOFTWARE("default_software", "Software", Item.SOFTWARE, null),
+    SOFTWARE("default_software", "Software", Item.SOFTWARE, SoftwareType.FEATURE_EXTRACTION),
     ARRAYDESIGN("default_arraydesign", "Array design", Item.ARRAYDESIGN, null),
     HYBRIDIZATION_HARDWARE("default_hybridization_hardware", "Hybridization station", Item.HARDWARE, HardwareType.HYBRIDIZATION_STATION),

trunk/src/core/net/sf/basedb/util/overview/ExperimentOverview.java

@@ -26 +26 @@
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import net.sf.basedb.core.Annotatable;
@@ -38 +41 @@
 import net.sf.basedb.core.ArrayDesign;
 import net.sf.basedb.core.ArraySlide;
+import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.BasicItem;
 import net.sf.basedb.core.BioSource;
@@ -44 +48 @@
 import net.sf.basedb.core.Extract;
 import net.sf.basedb.core.Hardware;
+import net.sf.basedb.core.HardwareType;
 import net.sf.basedb.core.Hybridization;
 import net.sf.basedb.core.Image;
 import net.sf.basedb.core.Include;
+import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Label;
 import net.sf.basedb.core.LabeledExtract;
+import net.sf.basedb.core.Nameable;
 import net.sf.basedb.core.PermissionDeniedException;
 import net.sf.basedb.core.Project;
 import net.sf.basedb.core.Protocol;
+import net.sf.basedb.core.ProtocolType;
 import net.sf.basedb.core.RawBioAssay;
 import net.sf.basedb.core.Sample;
@@ -59 +67 @@
 import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.Software;
+import net.sf.basedb.core.SoftwareType;
+import net.sf.basedb.core.Type;
+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;
 
 /**
@@ -85 +97 @@
 {
 
-  public static final Validator PROJECT_DEFAULT_VALIDATOR = new Validator(
-    "project.usenondefault", "Use of non-default value",
-    "Checks if a property is the same as the default specified for the active project",
-    "Use of non-default value", Severity.WARNING
-  );
-  
   private static Map<String, List<Validator>> validators;
 
@@ -101 +107 @@
           Arrays.asList(new Validator[] 
           {
-            PROJECT_DEFAULT_VALIDATOR
+            Validator.NONDEFAULT_RAWDATATYPE, Validator.NONDEFAULT_ARRAYDESIGN, 
+            Validator.NONDEFAULT_PROTOCOL, Validator.NONDEFAULT_HARDWARE, 
+            Validator.NONDEFAULT_SOFTWARE
           })
         );
@@ -108 +116 @@
           {
             Validator.MISSING_BIOSOURCE, Validator.MISSING_SAMPLE, Validator.MISSING_EXTRACT,
-            Validator.MISSING_HYBRIDIZATION, Validator.MISSING_SCAN, Validator.MISSING_ARRAYDESIGN, 
-            Validator.MISSING_PROTOCOL, Validator.MISSING_HARDWARE, Validator.MISSING_SOFTWARE,
-            Validator.MISSING_ARRAYSLIDE
+            Validator.MISSING_LABELED_EXTRACT, Validator.MISSING_HYBRIDIZATION, 
+            Validator.MISSING_SCAN, Validator.MISSING_ARRAYDESIGN, Validator.MISSING_PROTOCOL, 
+            Validator.MISSING_HARDWARE, Validator.MISSING_SOFTWARE,
+            Validator.MISSING_ARRAYSLIDE, Validator.MISSING_ARRAYBATCH
           })
         );
-      temp.put("Missing annotations",
+      temp.put("Annotations",
           Arrays.asList(new Validator[]
           {
             Validator.MISSING_MIAME_ANNOTATION, Validator.MISSING_FACTORVALUE, 
-            Validator.MISSING_PARAMETER
+            Validator.MISSING_PARAMETER, Validator.ANNOTATION_IS_PARAMETER, 
+            Validator.ANNOTATION_INVALID_VALUE, Validator.ANNOTATION_INVALID_ITEM,
+            Validator.ANNOTATION_INHERIT_FROM_NONPARENT, Validator.ANNOTATION_INHERIT_MULTIPLE
           })
         );
+      
+      temp.put("Denied access",
+          Arrays.asList(new Validator[]
+           {
+            Validator.DENIED_BIOSOURCE, Validator.DENIED_SAMPLE, Validator.DENIED_EXTRACT,
+            Validator.DENIED_LABEL, Validator.DENIED_HYBRIDIZATION, Validator.DENIED_SCAN,
+            Validator.DENIED_ARRAYDESIGN, Validator.DENIED_PROTOCOL, Validator.DENIED_HARDWARE,
+            Validator.DENIED_SOFTWARE, Validator.DENIED_ARRAYSLIDE, Validator.DENIED_ARRAYBATCH
+           })
+        );
+      
+      temp.put("Other",
+          Arrays.asList(new Validator[]
+          {
+            Validator.NONMATHCING_ARRAYDESIGN, Validator.MULTIPLE_ARRAYDESIGNS, 
+            Validator.INCORRECT_PROTOCOLTYPE, Validator.INCORRECT_SOFTWARETYPE,
+            Validator.INCORRECT_HARDWARETYPE, Validator.INCORRECT_NUM_LABELEDEXTRACTS,
+            Validator.NONUNIQUE_LABEL, Validator.DIFFERENT_LABEL, 
+            Validator.NONUNIQUE_NAME_FOR_TYPE, Validator.NONUNIQUE_NAME_GLOBAL,
+            Validator.CIRCULAR_REFERENCE
+          })
+        );
+      
       validators = Collections.unmodifiableMap(temp);
     }
@@ -161 +195 @@
   private ValidationOptions validationOptions;
   private List<Failure> failures;
+  private Map<String, Node> allNodes;
+  private Map<Item, Set<AnnotationType>> miameAnnotations;
+  private Map<Annotatable, Set<Annotatable>> annotatableParents;
   
   /**
@@ -187 +224 @@
   {
     this.experiment = Experiment.getById(dc, experiment.getId());
-    this.project = Project.getById(dc, project.getId());
+    this.project = project == null ? null : Project.getById(dc, project.getId());
     generateOverview(dc);
   }
@@ -197 +234 @@
   {
     this.failures = new LinkedList<Failure>();
+    this.annotatableParents = new HashMap<Annotatable, Set<Annotatable>>();
+    
+    // Load 'Required for MIAME' annotation types
+    ItemQuery<AnnotationType> query = initQuery(AnnotationType.getQuery(null), "name");
+    query.restrict(
+      Restrictions.eq(
+        Hql.property("requiredForMiame"), 
+        Expressions.parameter("flag", true, Type.BOOLEAN)
+      )
+    );
+    this.miameAnnotations = new HashMap<Item, Set<AnnotationType>>();
+    for (AnnotationType at : query.list(dc))
+    {
+      for (Item itemType : at.getEnabledItems())
+      {
+        Set<AnnotationType> types = miameAnnotations.get(itemType);
+        if (types == null)
+        {
+          types = new HashSet<AnnotationType>();
+          miameAnnotations.put(itemType, types);
+        }
+        types.add(at);
+      }
+    }
     
     // Node and subnodes
@@ -208 +269 @@
       if (experiment.getRawDataType() != project.getDefaultRawDataType())
       {
-        failures.add(new Failure(PROJECT_DEFAULT_VALIDATOR, rootNode));
-      }
-    }
+        failures.add(
+          new Failure(Validator.NONDEFAULT_RAWDATATYPE, rootNode, null,
+            new Fix("Change default raw data type of project", project)
+          )
+        );
+      }
+    }
+    
+    this.allNodes = new HashMap<String, Node>();
+    allNodes.put(rootNode.getId(), rootNode);
+    cacheChildNodes(rootNode);
+
+    // Validate the names of items
+    Map<String, Map<Item, List<Node>>> names = new HashMap<String, Map<Item, List<Node>>>();
+    Set<Node> nonUniqueGlobal = new HashSet<Node>();
+    Set<Node> nonUniqueForType = new HashSet<Node>();
+    for (Node node : allNodes.values())
+    {
+      if (node.getNodeType() == Node.Type.ITEM)
+      {
+        BasicItem item = node.getItem();
+        if (item instanceof Nameable)
+        {
+          String name = ((Nameable)item).getName();
+          Map<Item, List<Node>> typeMap = names.get(name);
+          if (typeMap != null)
+          {
+            List<Node> otherNodes = typeMap.get(item.getType());
+            if (otherNodes != null)
+            {
+              // Possible non-unique match; but check for self-match
+              if (!item.equals(otherNodes.get(0).getItem()))
+              {
+                nonUniqueForType.add(node);
+                for (Node otherNode : otherNodes)
+                {
+                  nonUniqueForType.add(otherNode);
+                }
+              }
+              else
+              {
+                otherNodes.add(node);
+              }
+            }
+            else
+            {
+              nonUniqueGlobal.add(node);
+              if (typeMap.size() == 1)
+              {
+                nonUniqueGlobal.add(typeMap.values().iterator().next().get(0));
+              }
+              List<Node> nodeList = new LinkedList<Node>();
+              nodeList.add(node);
+              typeMap.put(item.getType(), nodeList);
+            }
+          }
+          else
+          {
+            List<Node> nodeList = new LinkedList<Node>();
+            nodeList.add(node);
+            typeMap = new HashMap<Item, List<Node>>();
+            typeMap.put(item.getType(), nodeList);
+            names.put(name, typeMap);
+          }
+        }
+      }
+    }
+    names.clear();
+    
+    // Non-unique of same type
+    for (Node node : nonUniqueForType)
+    {
+      failures.add(new Failure(Validator.NONUNIQUE_NAME_FOR_TYPE, node, null,
+        new Fix("Change name of item", node.getItem())
+      ));
+    }
+    nonUniqueForType.clear();
+    
+    // Non-unique of different types
+    for (Node node : nonUniqueGlobal)
+    {
+      failures.add(new Failure(Validator.NONUNIQUE_NAME_GLOBAL, node, null,
+        new Fix("Change name of item", node.getItem())
+      ));
+    }
+    nonUniqueGlobal.clear();
+
     updateFailureCountOnNodes();
   }
@@ -228 +373 @@
   {
     return project;
+  }
+  
+  /**
+    Get the annotation types that have the 'Required for MIAME' flag
+    set to true and is enabled for the specified item type.
+    @param itemType The item type
+    @return An set containing the annotation types or null if no annotation
+      types exists
+  */
+  public Set<AnnotationType> getMiameAnnotationTypes(Item itemType)
+  {
+    return miameAnnotations.get(itemType);
+  }
+  
+  public Set<Annotatable> getAnnotatableParents(Annotatable item)
+  {
+    Set<Annotatable> parents = annotatableParents.get(item);
+    if (parents == null)
+    {
+      parents = new HashSet<Annotatable>();
+      annotatableParents.put(item, parents);
+      Set<Annotatable> temp = item.getAnnotatableParents();
+      if (temp != null)
+      {
+        for (Annotatable a : temp)
+        {
+          parents.add(a);
+          parents.addAll(getAnnotatableParents(a));
+        }
+      }
+    }
+    return parents;
   }
   
@@ -269 +446 @@
       }
     }
+  }
+  
+  private void cacheChildNodes(Node node)
+  {
+    if (node.getChildren() != null)
+    {
+      for (Node child : node.getChildren())
+      {
+        allNodes.put(child.getId(), child);
+        cacheChildNodes(child);
+      }
+    }
+  }
+  
+  public Node getNode(String nodeId)
+  {
+    return allNodes.get(nodeId);
   }
   
@@ -314 +508 @@
     Experiment experiment = (Experiment)rootNode.getItem();
     ItemQuery<RawBioAssay> rbaQuery = initQuery(experiment.getRawBioAssays(), "name");
+    Set<BasicItem> arrayDesigns = new HashSet<BasicItem>();
     for (RawBioAssay rba : rbaQuery.list(dc))
     {
-      addRawBioAssay(dc, rawBioAssaysNode, rba);
-    }
+      Node rbaNode = addRawBioAssay(dc, rawBioAssaysNode, rba);
+      Node adNode = rbaNode.getChild("arraydesign");
+      arrayDesigns.add(adNode == null ? null : adNode.getItem());
+    }
+    
+    // Check if all raw bioassays use the same array design
+    if (arrayDesigns.size() > 1)
+    {
+      failures.add(new Failure(Validator.MULTIPLE_ARRAYDESIGNS, rootNode));
+    }
+    
     return rawBioAssaysNode;
   }
@@ -329 +533 @@
   {
     Node rbaNode = new Node("rawbioassay."+rba.getId(), rba.getName(), rawBioAssaysNode, rba);
-    addAnnotations(dc, rbaNode);
-    addArrayDesign(dc, rbaNode);
-    addScan(dc, rbaNode);
+    Node annotationsNode = addAnnotations(dc, rbaNode);
+    Node adNode = addArrayDesign(dc, rbaNode);
+    Node scanNode = addScan(dc, rbaNode);
     addSoftware(dc, rbaNode);
-    addProtocol(dc, rbaNode);
+    addProtocol(dc, rbaNode, Project.Default.FEATURE_EXTRACTION_PROTOCOL);
+    
+    // Check for project default raw data type
+    if (project != null)
+    {
+      if (rba.getRawDataType() != project.getDefaultRawDataType())
+      {
+        failures.add(
+          new Failure(Validator.NONDEFAULT_RAWDATATYPE, rbaNode, null,
+            new Fix("Change default raw data type of project", project)
+          )
+        );
+      }
+    }
+    
+    // Check for missing experimental factor values
+    Node efNode = rootNode.getChild("experimental.factors");
+    if (efNode != null && efNode.getChildren() != null)
+    {
+      for (Node factorNode : efNode.getChildren())
+      {
+        Node annotationNode = annotationsNode.getChild("annotationtype." + factorNode.getItem().getId());
+        if (annotationNode == null)
+        {
+          AnnotationType at = (AnnotationType)factorNode.getItem();
+          Fix addFactor = at.isEnabledForItem(Item.RAWBIOASSAY) ?
+            new Fix("Add value to experimental factor", rba, at, false) :
+            new Fix("Inherit annotation from a parent item", rba, at, true);
+          failures.add(new Failure(Validator.MISSING_FACTORVALUE, rbaNode, 
+            "Missing factor value for " + at.getName(), addFactor));
+        }
+      }
+    }
+
+    // Check that the array design is same as hybridizations array design
+    Scan scan = scanNode == null ? null : (Scan)scanNode.getItem();
+    if (scan != null)
+    {
+      BasicItem ad1 = adNode == null ? null : adNode.getItem();
+      try
+      {
+        BasicItem ad2 = scan.getArrayDesign();
+        if ((ad1 == null && ad2 != null) || (ad1 != null && !ad1.equals(ad2)))
+        {
+          Fix fix = null;
+          try
+          {
+            Hybridization hyb = scan.getHybridization();
+            if (hyb != null) fix = new Fix("Change array slide of hybridization", hyb);
+          }
+          catch (PermissionDeniedException ex)
+          {}
+          failures.add(new Failure(Validator.NONMATHCING_ARRAYDESIGN, rbaNode, null,
+            fix));
+        }
+      }
+      catch (PermissionDeniedException ex)
+      {}
+    }
+    
     return rbaNode;
   }
@@ -360 +623 @@
     {
       adNode = new Node("arraydesign", "Array design: denied", parentNode, null);
+      failures.add(new Failure(Validator.DENIED_ARRAYDESIGN, adNode));
     }
     if (ad != null)
     {
       adNode = new Node("arraydesign", "Array design: " + ad.getName(), parentNode, ad);
+      
+      // Check if the array design is the same as the project default
+      if (project != null)
+      {
+        try
+        {
+          BasicItem defaultItem = project.getDefaultItem(dc, Project.Default.ARRAYDESIGN);
+          if (defaultItem != null && !ad.equals(defaultItem))
+          {
+            failures.add(new Failure(Validator.NONDEFAULT_ARRAYDESIGN, parentNode, null,
+              new Fix("Change default array design for project", project)));
+          }
+        }
+        catch (BaseException ex)
+        {}
+      }
     }
     if (adNode == null)
@@ -388 +668 @@
     {
       scanNode = new Node("scan", "Scan: denied", rawBioAssayNode, null);
+      failures.add(new Failure(Validator.DENIED_SCAN, scanNode));
     }
     if (scan != null)
@@ -397 +678 @@
       addHardware(dc, scanNode, "Scanner");
       addHybridization(dc, scanNode);
-      addProtocol(dc, scanNode);
+      addProtocol(dc, scanNode, Project.Default.SCANNING_PROTOCOL);
     }
     if (scanNode == null)
     {
-      failures.add(new Failure(Validator.MISSING_SCAN, rawBioAssayNode));
+      failures.add(new Failure(Validator.MISSING_SCAN, rawBioAssayNode, null,
+        new Fix("Add scan to raw bioassay", rba)));
     }
     return scanNode;
@@ -422 +704 @@
     {
       hybNode = new Node("hybridization", "Hybridization: denied", scanNode, null);
+      failures.add(new Failure(Validator.DENIED_HYBRIDIZATION, hybNode));
     }
     if (scan != null)
@@ -429 +712 @@
       addLabeledExtracts(dc, hybNode);
       addHardware(dc, hybNode, "Hyb. station");
-      addProtocol(dc, hybNode);
+      addProtocol(dc, hybNode, Project.Default.HYBRIDIZATION_PROTOCOL);
       addArraySlide(dc, hybNode);
     }
     if (hybNode == null)
     {
-      failures.add(new Failure(Validator.MISSING_HYBRIDIZATION, scanNode));
+      failures.add(new Failure(Validator.MISSING_HYBRIDIZATION, scanNode, null,
+        new Fix("Add hybridization to scan", scan)));
     }
     return hybNode;
@@ -479 +763 @@
     ItemQuery<LabeledExtract> leQuery = 
       (ItemQuery<LabeledExtract>)initQuery(hyb.getCreationEvent().getSources(), "label.name");
+    int added = 0;
+    int channels = experiment.getRawDataType().getChannels();
+
+    Map<Label, LabeledExtract> labels = new HashMap<Label, LabeledExtract>();
+    Set<LabeledExtract> nonUnique = new HashSet<LabeledExtract>();
     for (LabeledExtract le : leQuery.list(dc))
     {
-      addLabeledExtract(dc, leNode, le);
+      Node llNode = addLabeledExtract(dc, leNode, le);
+      ++added;
+      try
+      {
+        Label l = le.getLabel();
+        if (labels.containsKey(l))
+        {
+          nonUnique.add(le);
+          nonUnique.add(labels.get(l));
+        }
+        else
+        {
+          labels.put(l, le);
+        }
+      }
+      catch (PermissionDeniedException ex)
+      {}
+    }
+    
+    // Check number of labeled extracts
+    if (added != channels)
+    {
+      Fix fix = added > channels ?
+        new Fix("Remove labeled extracts from hybridization", hyb) :
+        new Fix("Add labeled extracts to hybridization", hyb);
+      String message = added > channels ?
+        "Too many labeled extracts" : "Too few labeled extracts";
+      failures.add(new Failure(Validator.INCORRECT_NUM_LABELEDEXTRACTS, hybNode, message, fix));
+    }
+    
+    // Check that labeled extracts has unique labels
+    if (nonUnique.size() > 0)
+    {
+      Failure failure = new Failure(Validator.NONUNIQUE_LABEL, hybNode);
+      failure.addFix(new Fix("Change labeled extracts on hybridization", hyb));
+      for (LabeledExtract le : nonUnique)
+      {
+        failure.addFix(new Fix("Change label of " + le.getName(), le));
+      }
+      failures.add(failure);
     }
     return leNode;
@@ -501 +829 @@
     {}
     Node leNode = new Node("labeledextract."+le.getId(), 
-      (label != null ? le.getName() + ": " : "") + le.getName(), parentNode, le);
+      (label != null ? label.getName() + ": " : "") + le.getName(), parentNode, le);
+    
+    if (label == null)
+    {
+      failures.add(new Failure(Validator.DENIED_LABEL, leNode));
+    }
     
     addAnnotations(dc, leNode);
     if (le.isPooled())
     {
-      // addPooledLabledExtracts(dc, leNode);
+      addPooledLabeledExtracts(dc, leNode);
     }
     else
@@ -512 +845 @@
       addExtract(dc, leNode, null);
     }
-    addProtocol(dc, leNode);
+    addProtocol(dc, leNode, Project.Default.LABELING_PROTOCOL);
     return leNode;
+  }
+  
+  /**
+    Add labeled extract child nodes that are the source labeled
+    extracts of a pooled labeled extract
+  */
+  @SuppressWarnings("unchecked")
+  private void addPooledLabeledExtracts(DbControl dc, Node parentNode)
+  {
+    LabeledExtract product = (LabeledExtract)parentNode.getItem();
+    Label productLabel = null;
+    try
+    {
+      productLabel = product.getLabel();
+    }
+    catch (PermissionDeniedException ex)
+    {}
+    
+    ItemQuery<LabeledExtract> sourceQuery = 
+      initQuery((ItemQuery<LabeledExtract>)product.getCreationEvent().getSources(), "name");
+    
+    int added = 0;
+    for (LabeledExtract source : sourceQuery.list(dc))
+    {
+      ++added;
+
+      // Check circular reference
+      boolean circular = false;
+      Node tempNode = parentNode;
+      BasicItem tempItem = tempNode.getItem();
+      while (tempNode != null && tempItem != null && tempItem.getType() == Item.LABELEDEXTRACT)
+      {
+        if (source.equals(tempItem))
+        {
+          failures.add(new Failure(Validator.CIRCULAR_REFERENCE, parentNode, 
+            "Circular reference to " + ((LabeledExtract)tempItem).getName(), 
+            new Fix("Modify source labeled extracts", product)
+          ));
+          tempNode = null;
+          tempItem = null;
+          circular = true;
+        }
+        else
+        {
+          tempNode = tempNode.getParent();
+          tempItem = tempNode.getItem();
+        }
+      }
+      
+      if (!circular)
+      {
+        Node leNode = addLabeledExtract(dc, parentNode, source);
+        
+        // Check that source has same label as product
+        if (productLabel != null)
+        {
+          try
+          {
+            Label label = source.getLabel();
+            if (!productLabel.equals(label))
+            {
+              failures.add(new Failure(Validator.DIFFERENT_LABEL, leNode, null,
+                new Fix("Change label of " + source.getName(), source),
+                new Fix("Change label of " + product.getName(), product)
+                ));
+            }
+          }
+          catch (PermissionDeniedException ex)
+          {}
+        }
+      }
+    }
+    
+    if (added == 0)
+    {
+      failures.add(new Failure(Validator.MISSING_LABELED_EXTRACT, parentNode, null,
+        new Fix("Add sources to the labeled extract", product)
+      ));
+    }
+    
   }
   
@@ -533 +946 @@
       {
         extractNode = new Node("extract", "Extract: denied", parentNode, null);
+        failures.add(new Failure(Validator.DENIED_EXTRACT, extractNode));
       }
       if (extract != null)
@@ -550 +964 @@
       if (extract.isPooled())
       {
-        // addPooledExtracts(dc, leNode);
+        addPooledExtracts(dc, extractNode);
       }
       else
@@ -556 +970 @@
         addSample(dc, extractNode, null);
       }
-      addProtocol(dc, extractNode);
+      addProtocol(dc, extractNode, Project.Default.EXTRACTING_PROTOCOL);
     }
     if (extractNode == null)
     {
-      failures.add(new Failure(Validator.MISSING_EXTRACT, parentNode));
+      failures.add(new Failure(Validator.MISSING_EXTRACT, parentNode, null,
+        new Fix("Add extract to labeled extract", parentNode.getItem())));
     }
     return extractNode;
+  }
+  
+  /**
+    Add extract child nodes that are the source extracts of a pooled extract.
+  */
+  @SuppressWarnings("unchecked")
+  private void addPooledExtracts(DbControl dc, Node parentNode)
+  {
+    Extract product = (Extract)parentNode.getItem();
+    
+    ItemQuery<Extract> sourceQuery = 
+      initQuery((ItemQuery<Extract>)product.getCreationEvent().getSources(), "name");
+    
+    int added = 0;
+    for (Extract source : sourceQuery.list(dc))
+    {
+      ++added;
+  
+      // Check circular reference
+      boolean circular = false;
+      Node tempNode = parentNode;
+      BasicItem tempItem = tempNode.getItem();
+      while (tempNode != null && tempItem != null && tempItem.getType() == Item.EXTRACT)
+      {
+        if (source.equals(tempItem))
+        {
+          failures.add(new Failure(Validator.CIRCULAR_REFERENCE, parentNode, 
+            "Circular reference to " + ((Extract)tempItem).getName(), 
+            new Fix("Modify source extracts", product)
+          ));
+          tempNode = null;
+          tempItem = null;
+          circular = true;
+        }
+        else
+        {
+          tempNode = tempNode.getParent();
+          tempItem = tempNode.getItem();
+        }
+      }
+      
+      if (!circular)
+      {
+        Node extractNode = addExtract(dc, parentNode, source);
+      }
+    }
+    
+    if (added == 0)
+    {
+      failures.add(new Failure(Validator.MISSING_EXTRACT, parentNode, null,
+        new Fix("Add sources to the extract", product)
+      ));
+    }
   }
   
@@ -582 +1050 @@
       {
         sampleNode = new Node("sample", "Sample: denied", parentNode, null);
+        failures.add(new Failure(Validator.DENIED_SAMPLE, sampleNode));
       }
       if (extract != null)
@@ -599 +1068 @@
       if (sample.isPooled())
       {
-        // addPooledSamples(dc, leNode);
+        addPooledSamples(dc, sampleNode);
       }
       else
@@ -605 +1074 @@
         addBioSource(dc, sampleNode);
       }
-      addProtocol(dc, sampleNode);
+      addProtocol(dc, sampleNode, Project.Default.SAMPLING_PROTOCOL);
     }
     if (sampleNode == null)
     {
-      failures.add(new Failure(Validator.MISSING_SAMPLE, parentNode));
+      failures.add(new Failure(Validator.MISSING_SAMPLE, parentNode, null,
+        new Fix("Add sample to extract", parentNode.getItem())));
     }
     return sampleNode;
+  }
+  
+  /**
+    Add sample child nodes that are the source samples of a pooled sample.
+  */
+  @SuppressWarnings("unchecked")
+  private void addPooledSamples(DbControl dc, Node parentNode)
+  {
+    Sample product = (Sample)parentNode.getItem();
+    
+    ItemQuery<Sample> sourceQuery = 
+      initQuery((ItemQuery<Sample>)product.getCreationEvent().getSources(), "name");
+    
+    int added = 0;
+    for (Sample source : sourceQuery.list(dc))
+    {
+      ++added;
+  
+      // Check circular reference
+      boolean circular = false;
+      Node tempNode = parentNode;
+      BasicItem tempItem = tempNode.getItem();
+      while (tempNode != null && tempItem != null && tempItem.getType() == Item.SAMPLE)
+      {
+        if (source.equals(tempItem))
+        {
+          failures.add(new Failure(Validator.CIRCULAR_REFERENCE, parentNode, 
+            "Circular reference to " + ((Sample)tempItem).getName(), 
+            new Fix("Modify source samples", product)
+          ));
+          tempNode = null;
+          tempItem = null;
+          circular = true;
+        }
+        else
+        {
+          tempNode = tempNode.getParent();
+          tempItem = tempNode.getItem();
+        }
+      }
+      
+      if (!circular)
+      {
+        Node sampleNode = addSample(dc, parentNode, source);
+      }
+    }
+    
+    if (added == 0)
+    {
+      failures.add(new Failure(Validator.MISSING_SAMPLE, parentNode, null,
+        new Fix("Add sources to the sample", product)
+      ));
+    }
   }
   
@@ -630 +1153 @@
     {
       bioSourceNode = new Node("biosource", "Biosource: denied", sampleNode, null);
+      failures.add(new Failure(Validator.DENIED_BIOSOURCE, bioSourceNode));
     }
     if (bioSource != null)
@@ -638 +1162 @@
     if (bioSourceNode == null)
     {
-      failures.add(new Failure(Validator.MISSING_BIOSOURCE, sampleNode));
+      failures.add(new Failure(Validator.MISSING_BIOSOURCE, sampleNode, null,
+        new Fix("Add biosource to sample", sampleNode.getItem())));
     }
     return bioSourceNode;
@@ -659 +1184 @@
     {
       slideNode = new Node("slide", "Array slide: denied", hybNode, null);
+      failures.add(new Failure(Validator.DENIED_ARRAYSLIDE, slideNode));
     }
     if (slide != null)
@@ -668 +1194 @@
     if (slideNode == null)
     {
-      failures.add(new Failure(Validator.MISSING_ARRAYSLIDE, hybNode));
+      failures.add(new Failure(Validator.MISSING_ARRAYSLIDE, hybNode, null,
+        new Fix("Add array slide to hybridization", hyb)));
     }
     return slideNode;
@@ -689 +1216 @@
     {
       batchNode = new Node("batch", "Batch: denied", slideNode, null);
+      failures.add(new Failure(Validator.DENIED_ARRAYBATCH, batchNode));
     }
     if (batch != null)
@@ -696 +1224 @@
       addArrayDesign(dc, batchNode);
       addHardware(dc, batchNode, "Print robot");
-      addProtocol(dc, batchNode);
+      addProtocol(dc, batchNode, Project.Default.PRINTING_PROTOCOL);
+    }
+    if (batchNode == null)
+    {
+      failures.add(new Failure(Validator.MISSING_ARRAYBATCH, slideNode));
     }
     return batchNode;
@@ -710 +1242 @@
     Software software = null;
     Node softwareNode = null;
+    Project.Default projectDefault = null;
     try
     {
@@ -715 +1248 @@
       {
         software = ((RawBioAssay)item).getSoftware();
+        projectDefault = Project.Default.SOFTWARE;
       }
     }
@@ -720 +1254 @@
     {
       softwareNode = new Node("software", "Software: denied", parentNode, null);
+      failures.add(new Failure(Validator.DENIED_SOFTWARE, softwareNode));
     }
     if (software != null)
     {
       softwareNode = new Node("software", "Software: " + software.getName(), parentNode, software);
+
+      // Check if using project default software
+      if (project != null && projectDefault != null)
+      {
+        try
+        {
+          BasicItem defaultItem = project.getDefaultItem(dc, projectDefault);
+          if (defaultItem != null && !software.equals(defaultItem))
+          {
+            failures.add(new Failure(Validator.NONDEFAULT_SOFTWARE, parentNode, null,
+                new Fix("Change software of raw bioassay", item),
+                new Fix("Change default software of project", project)
+              ));
+          }
+        }
+        catch (BaseException ex)
+        {}
+      }
+      
+      // Check hardware type
+      try
+      {
+        SoftwareType st = software.getSoftwareType();
+        if (!st.getSystemId().equals(projectDefault.getType()))
+        {
+          failures.add(new Failure(Validator.INCORRECT_SOFTWARETYPE, parentNode, null,
+            new Fix("Change software of raw bioassay", item),
+            new Fix("Change type of software", software)
+          ));
+        }
+      }
+      catch (PermissionDeniedException ex)
+      {}
+      
     }
     if (softwareNode == null)
     {
-      failures.add(new Failure(Validator.MISSING_SOFTWARE, parentNode));
+      failures.add(new Failure(Validator.MISSING_SOFTWARE, parentNode, null,
+        new Fix("Add software to raw bioassay", item)));
     }
     return softwareNode;
@@ -739 +1309 @@
   {
     BasicItem item = parentNode.getItem();
+    String itemTypeName = item.getType().toString().toLowerCase();
     Hardware hardware = null;
     Node hardwareNode = null;
+    Project.Default projectDefault = null;
     try
     {
@@ -747 +1319 @@
       {
         hardware = ((Scan)item).getScanner();
+        projectDefault = Project.Default.SCANNER_HARDWARE;
       }
       else if (itemType == Item.HYBRIDIZATION)
       {
         hardware = ((Hybridization)item).getCreationEvent().getHardware();
+        projectDefault = Project.Default.HYBRIDIZATION_HARDWARE;
       }
       else if (itemType == Item.ARRAYBATCH)
       {
         hardware = ((ArrayBatch)item).getPrintRobot();
+        projectDefault = Project.Default.PRINTROBOT_HARDWARE;
       }
     }
@@ -760 +1335 @@
     {
       hardwareNode = new Node("hardware", hardwareType + ": denied", parentNode, null);
+      failures.add(new Failure(Validator.DENIED_HARDWARE, hardwareNode));
     }
     if (hardware != null)
     {
       hardwareNode = new Node("hardware", hardwareType + ": " + hardware.getName(), parentNode, hardware);
+      
+      // Check if using project default hardware
+      if (project != null && projectDefault != null)
+      {
+        try
+        {
+          BasicItem defaultItem = project.getDefaultItem(dc, projectDefault);
+          if (defaultItem != null && !hardware.equals(defaultItem))
+          {
+            failures.add(new Failure(Validator.NONDEFAULT_HARDWARE, parentNode, null,
+              new Fix("Change " + hardwareType.toLowerCase() + " of " + itemTypeName, item),
+              new Fix("Change default " + hardwareType.toLowerCase() + " of project", project)
+            ));
+          }
+        }
+        catch (BaseException ex)
+        {}
+      }
+      
+      // Check hardware type
+      try
+      {
+        HardwareType ht = hardware.getHardwareType();
+        if (!ht.getSystemId().equals(projectDefault.getType()))
+        {
+          failures.add(new Failure(Validator.INCORRECT_HARDWARETYPE, parentNode, null,
+            new Fix("Change " + hardwareType + " of " + itemTypeName, item),
+            new Fix("Change type of " + hardwareType, hardware)
+          ));
+        }
+      }
+      catch (PermissionDeniedException ex)
+      {}
+
     }
     if (hardwareNode == null)
     {
-      failures.add(new Failure(Validator.MISSING_HARDWARE, parentNode));
+      failures.add(new Failure(Validator.MISSING_HARDWARE, parentNode, null,
+        new Fix("Add " + hardwareType.toLowerCase() + " to " + item.getType().toString().toLowerCase(), item)));
     }
     return hardwareNode;
@@ -776 +1387 @@
     Creates an item-type node with the name <code>protocol</code>.
   */
-  private Node addProtocol(DbControl dc, Node parentNode)
+  private Node addProtocol(DbControl dc, Node parentNode, Project.Default defaultProtocol)
   {
     BasicItem item = parentNode.getItem();
@@ -791 +1402 @@
     {
       protocolNode = new Node("protocol", "Protocol: denied", parentNode, null);
+      failures.add(new Failure(Validator.DENIED_PROTOCOL, protocolNode));
     }
     if (protocol != null)
@@ -796 +1408 @@
       protocolNode = new Node("protocol", "Protocol: " + protocol.getName(), parentNode, protocol);
       addProtocolParameters(dc, protocolNode);
+      
+      // Check if using project default protocol
+      if (project != null)
+      {
+        try
+        {
+          BasicItem defaultItem = project.getDefaultItem(dc, defaultProtocol);
+          if (defaultItem != null && !protocol.equals(defaultItem))
+          {
+            failures.add(new Failure(Validator.NONDEFAULT_PROTOCOL, parentNode, null,
+              new Fix("Change protocol of " + item.getType().toString().toLowerCase(), item),
+              new Fix("Change default " + defaultProtocol.getShortName().toLowerCase() + " for project", project)
+            ));
+          }
+        }
+        catch (BaseException ex)
+        {}
+      }
+      
+      // Check protocol type
+      try
+      {
+        ProtocolType pt = protocol.getProtocolType();
+        if (!pt.getSystemId().equals(defaultProtocol.getType()))
+        {
+          failures.add(new Failure(Validator.INCORRECT_PROTOCOLTYPE, parentNode, null,
+            new Fix("Change protocol of " + item.getType().toString().toLowerCase(), item),
+            new Fix("Change type of protocol", protocol)
+          ));
+        }
+      }
+      catch (PermissionDeniedException ex)
+      {}
     }
     if (protocolNode == null)
     {
-      failures.add(new Failure(Validator.MISSING_PROTOCOL, parentNode));
+      failures.add(new Failure(Validator.MISSING_PROTOCOL, parentNode, null,
+        new Fix("Add protocol to " + item.getType().toString().toLowerCase(), item)));
     }
     return protocolNode;
@@ -814 +1460 @@
   {
     Protocol protocol = (Protocol)protocolNode.getItem();
+    Node parentNode = protocolNode.getParent();
+    BasicItem parentItem = parentNode.getItem();
+    Annotatable annotatable = parentItem instanceof Annotatable ? (Annotatable)parentItem : null;
+    AnnotationSet as = annotatable != null && annotatable.isAnnotated() ? 
+        annotatable.getAnnotationSet() : null;
     ItemQuery<AnnotationType> parameterQuery = initQuery(protocol.getParameters(), "name");
     List<AnnotationType> parameters = parameterQuery.list(dc);
@@ -823 +1474 @@
       {
         new Node("parameter."+pp.getId(), pp.getName(), parameterNode, pp);
+        
+        // Check if a value for this parameter has been specified
+        if (as != null && !as.hasAnnotation(pp))
+        {
+          failures.add(new Failure(Validator.MISSING_PARAMETER, parentNode, 
+            "Missing parameter value: " + pp.getName(), 
+            new Fix("Add parameter value", parentItem, pp, false)));
+        }
       }
     }
@@ -841 +1500 @@
     if (parent.isAnnotated())
     {
+      Protocol protocol = null;
+      try
+      {
+        protocol = parent.getProtocol();
+      }
+      catch (PermissionDeniedException ex)
+      {}
       annotationsNode = new Node("annotations", "Annotations", parentNode);
       AnnotationSet as = parent.getAnnotationSet();
       ItemQuery<Annotation> annotationQuery = initQuery(as.getAnnotations(), "annotationType.name");
+      Map<AnnotationType, Node> annotationTypes = new HashMap<AnnotationType, Node>();
+      Set<AnnotationType> duplicates = new HashSet<AnnotationType>();
+    
       for (Annotation a : annotationQuery.list(dc))
       {
-        AnnotationType at = a.getAnnotationType();
-        new Node("annotation."+at.getId(), at.getName(), annotationsNode, at);
-      }
+        try
+        {
+          AnnotationType at = a.getAnnotationType();
+          if (protocol == null || protocol.isParameter(at))
+          {
+            Node atNode = new Node("annotationtype."+at.getId(), at.getName(), annotationsNode, at);
+            annotationTypes.put(at, atNode);
+            
+            // Check if annotation is a protocol parameter
+            if (at.isProtocolParameter())
+            {
+              failures.add(new Failure(Validator.ANNOTATION_IS_PARAMETER, parentNode, 
+                "Annotation " + at.getName() + " is a protocol parameter",
+                new Fix("Remove annotation value", (BasicItem)parent, at, false),
+                new Fix("Change 'parameter' flag of annotation type", at)
+              ));
+            }
+            
+            // Check if annotation can be used on this item type
+            if (!at.isEnabledForItem(parent.getType()))
+            {
+              failures.add(new Failure(Validator.ANNOTATION_INVALID_ITEM, parentNode, 
+                "Annotation " + at.getName() + " is invalid for item type: " + parent.getType(), 
+                new Fix("Remove annotation value", (BasicItem)parent, at, false),
+                new Fix("Add '" + parent.getType().name() + "' to annotation type", at)
+              ));
+            }
+            try
+            {
+              List<?> values = a.getValues();
+              if (values != null)
+              {
+                for (Object value : values)
+                {
+                  at.validateAnnotationValue(value);
+                }
+              }
+            }
+            catch (InvalidDataException ex)
+            {
+              failures.add(new Failure(Validator.ANNOTATION_INVALID_VALUE, parentNode, ex.getMessage(),
+                new Fix("Change annotation value", (BasicItem)parent, at, false),
+                new Fix("Change annotation type restrictions", at)
+              ));
+            }
+          }
+        }
+        catch (PermissionDeniedException ex)
+        {
+          Node annotationNode = new Node("annotation."+a.getId(), a.getValueType().toString(), annotationsNode, a);
+          failures.add(new Failure(Validator.DENIED_ANNOTATIONTYPE, annotationNode));
+        }
+      }
+      
+      // Check if all MIAME annotations are specified
+      Set<AnnotationType> miameAnnotations = getMiameAnnotationTypes(parent.getType());
+      if (miameAnnotations != null)
+      {
+        for (AnnotationType at : miameAnnotations)
+        {
+          if (!annotationTypes.containsKey(at))
+          {
+            failures.add(new Failure(Validator.MISSING_MIAME_ANNOTATION, parentNode, null, 
+                new Fix("Add value for annotation " + at.getName(), (BasicItem)parent, at, false),
+                new Fix("Remove 'Required for MIAME' flag on " + at.getName(), at)
+              ));
+          }
+        }
+      }
+      annotationTypes.clear();
       
       annotationQuery = initQuery(as.getAllInheritedAnnotations(), "annotationType.name");
-      for (Annotation a : annotationQuery.list(dc))
-      {
-        AnnotationType at = a.getAnnotationType();
-        new Node("annotation."+at.getId(), at.getName(), annotationsNode, at);
-      }     
-    }
+      List<Annotation> inherited = annotationQuery.list(dc);
+      if (inherited.size() > 0)
+      {
+        Set<Annotatable> parents = getAnnotatableParents(parent);
+
+        for (Annotation a : inherited)
+        {
+          Node atNode = null;
+          AnnotationType at = null;
+          try
+          {
+            at = a.getAnnotationType();
+            atNode = new Node("annotationtype."+at.getId(), at.getName(), annotationsNode, at);
+            if (annotationTypes.containsKey(at))
+            {
+              duplicates.add(at);
+            }
+            else
+            {
+              annotationTypes.put(at, atNode);
+            }
+          }
+          catch (PermissionDeniedException ex)
+          {
+            atNode = new Node("annotation."+a.getId(), a.getValueType().toString(), annotationsNode, a);
+            failures.add(new Failure(Validator.DENIED_ANNOTATIONTYPE, atNode));
+          }
+          try
+          {
+            Annotatable inheritFrom = a.getAnnotationSet().getItem();
+            if (!parents.contains(inheritFrom))
+            {
+              failures.add(new Failure(Validator.ANNOTATION_INHERIT_FROM_NONPARENT, parentNode, 
+                "Inheriting annotation " + (at != null ? 
+                  at.getName() : a.getValueType().toString()) + " from non-parent",
+                new Fix("Remove inherited annotation", parentNode.getItem(), at, true)
+              ));
+            }
+          }
+          catch (PermissionDeniedException ex)
+          {}
+        }
+      }
+      
+      // Add warnings for duplicate annotation types
+      if (duplicates.size() > 0)
+      {
+        for (AnnotationType dup : duplicates)
+        {
+          failures.add(new Failure(Validator.ANNOTATION_INHERIT_MULTIPLE, parentNode, 
+            "Inherits multiple annotations of type " + dup.getName(),
+            new Fix("Modify inherited annotations", parentNode.getItem(), dup, true)
+          ));
+        }
+      }
+      
+    }
+
     return annotationsNode;
   }
-
 
   /**

trunk/src/core/net/sf/basedb/util/overview/Failure.java

@@ -24 +24 @@
 package net.sf.basedb.util.overview;
 
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+
 /**
   Holds information about a failed validation. Note that all 
@@ -43 +47 @@
   private Validator validator;
   private Node node;
+  private String message;
+  private List<Fix> fixes;
   
   /**
@@ -51 +57 @@
   public Failure(Validator validator, Node node)
   {
+    this(validator, node, null, (Fix[])null);
+  }
+  
+  public Failure(Validator validator, Node node, String message)
+  {
+    this(validator, node, message, (Fix[])null);
+  }
+  
+  public Failure(Validator validator, Node node, String message, Fix... fixes)
+  {
     this.validator = validator;
     this.node = node;
+    this.message = message;
+    this.fixes = new LinkedList<Fix>();
+    if (fixes != null) this.fixes.addAll(Arrays.asList(fixes));
   }
   
@@ -71 +90 @@
   }
   
+  /**
+    Get a message explaining the failure.
+  */
+  public String getMessage()
+  {
+    return message != null ? message : validator.getFailureSummary();
+  }
+  
+  public List<Fix> getFixes()
+  {
+    return fixes;
+  }
+  
+  public void addFix(Fix fix)
+  {
+    fixes.add(fix);
+  }
+  
+  public String toString()
+  {
+    return getMessage();
+  }
 }

trunk/src/core/net/sf/basedb/util/overview/Validator.java

@@ -49 +49 @@
 
   /**
+    Validator rule that checks for denied access to protocols. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_PROTOCOL = new Validator(
+      "denied.protocol", "Access denied to protocol", 
+      "Checks if the user is denied access to a protocol",
+      "Access denied to protocol", Severity.WARNING
+    );
+
+  /**
     Validator rule that checks for missing scan. Default severity level
     is WARNING.
@@ -59 +69 @@
   
   /**
+    Validator rule that checks for denied access to scans. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_SCAN = new Validator(
+      "denied.scan", "Access denied to scan", 
+      "Checks if the user is denied access to a scan",
+      "Access denied to scan", Severity.WARNING
+    );
+  
+  /**
     Validator rule that checks for missing software. Default severity level
     is WARNING.
@@ -66 +86 @@
       "Checks if a software has been specified for a raw bioassay",
       "Missing software", Severity.WARNING
+    );
+  
+  /**
+    Validator rule that checks for denied access to software. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_SOFTWARE = new Validator(
+      "denied.software", "Access denied to software", 
+      "Checks if the user is denied access to a software",
+      "Access denied to software", Severity.WARNING
     );
   
@@ -80 +110 @@
 
   /**
+    Validator rule that checks for denied access to hardware. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_HARDWARE = new Validator(
+      "denied.hardware", "Access denied to hardware", 
+      "Checks if the user is denied access to a hardware",
+      "Access denied to hardware", Severity.WARNING
+    );
+
+  /**
     Validator rule that checks for missing hybridization. Default severity level
     is WARNING.
@@ -90 +130 @@
 
   /**
+    Validator rule that checks for denied access to hybridization. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_HYBRIDIZATION = new Validator(
+      "denied.hybridization", "Access denied to hybridization", 
+      "Checks if the user is denied access to a hybridization",
+      "Access denied to hybridization", Severity.WARNING
+    );
+
+  /**
     Validator rule that checks for missing array slide. Default severity level
     is WARNING.
@@ -100 +150 @@
 
   /**
+    Validator rule that checks for denied access to array slides. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_ARRAYSLIDE = new Validator(
+      "denied.slide", "Access denied to array slide", 
+      "Checks if the user is denied access to an array slide",
+      "Access denied to array slide", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks for missing labeled extract. Default severity level
+    is WARNING.
+  */
+  public static final Validator MISSING_LABELED_EXTRACT = new Validator(
+      "missing.labeledextract", "Missing labeled extract", 
+      "Checks if at least one labeled extract has been specified as parent to a " +
+      "pooled labeled extract",
+      "Missing labeled extract", Severity.WARNING
+    );
+  
+  /**
     Validator rule that checks for missing extract. Default severity level
     is WARNING.
@@ -105 +176 @@
   public static final Validator MISSING_EXTRACT = new Validator(
       "missing.extract", "Missing extract", 
-      "Checks if an extract has been specified for a non-pooled labled extract",
+      "Checks if an extract has been specified for a labled extract or pooled extract",
       "Missing extract", Severity.WARNING
     );
 
+  /**
+    Validator rule that checks for denied access to extracts. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_EXTRACT = new Validator(
+      "denied.extract", "Access denied to extract", 
+      "Checks if the user is denied access to a extract",
+      "Access denied to extract", Severity.WARNING
+    );
+
+  
   /**
     Validator rule that checks for missing sample. Default severity level
@@ -115 +197 @@
   public static final Validator MISSING_SAMPLE = new Validator(
       "missing.sample", "Missing sample", 
-      "Checks if a sample has been specified for a non-pooled extract",
+      "Checks if a sample has been specified for an extract or pooled sample",
       "Missing sample", Severity.WARNING
     );
 
+  /**
+    Validator rule that checks for denied access to samples. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_SAMPLE = new Validator(
+      "denied.sample", "Access denied to sample", 
+      "Checks if the user is denied access to a sample",
+      "Access denied to sample", Severity.WARNING
+    );
+
+  
   /**
     Validator rule that checks for missing biosource. Default severity level
@@ -130 +223 @@
 
   /**
+    Validator rule that checks for denied access to biosource. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_BIOSOURCE = new Validator(
+      "denied.biosource", "Access denied to biosource", 
+      "Checks if the user is denied access to a biosource",
+      "Access denied to biosource", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks for denied access to labels. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_LABEL = new Validator(
+      "denied.label", "Access denied to label", 
+      "Checks if the user is denied access to a label",
+      "Access denied to label", Severity.WARNING
+    );
+  
+  /**
     Validator rule that checks for missing array design. Default severity level
     is WARNING.
   */
   public static final Validator MISSING_ARRAYDESIGN = new Validator(
-      "missing.arraydesign", "Missing arraydesign", 
+      "missing.arraydesign", "Missing array design", 
       "Checks if an array design has been specified for a raw bioassay",
       "Missing array design", Severity.WARNING
@@ -140 +253 @@
 
   /**
+    Validator rule that checks for denied access to an array design. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_ARRAYDESIGN = new Validator(
+      "denied.arraydesign", "Access denied to array design", 
+      "Checks if the user is denied access to an array design",
+      "Access denied to array design", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks for missing array batch. Default severity level
+    is WARNING.
+  */
+  public static final Validator MISSING_ARRAYBATCH = new Validator(
+      "missing.arraybatch", "Missing array batch", 
+      "Checks if an array batch has been specified for an array slide",
+      "Missing array batch", Severity.WARNING
+    );
+  
+  /**
+    Validator rule that checks for denied access to an array batch. Default severity level
+    is WARNING.
+  */
+  public static final Validator DENIED_ARRAYBATCH = new Validator(
+      "denied.arraybatch", "Access denied to array batch", 
+      "Checks if the user is denied access to an array batch",
+      "Access denied to array batch", Severity.WARNING
+    );
+
+  
+  /**
     Validator rule that checks for missing experimental factor value. 
     Default severity level is ERROR.
@@ -145 +289 @@
   public static final Validator MISSING_FACTORVALUE = new Validator(
       "missing.factorvalue", "Missing factor value", 
-      "Checks if a factorvalue has been specified for a raw bioassay",
+      "Checks if a value has been specified for all experimental factors for a raw bioassay",
       "Missing factor value", Severity.ERROR
     );
@@ -155 +299 @@
   public static final Validator MISSING_PARAMETER = new Validator(
       "missing.parameter", "Missing parameter value", 
-      "Checks if a parameter has been specified for a protocol",
+      "Checks if a parameter value has been specified for all protocol parameters",
       "Missing parameter value", Severity.ERROR
     );
 
   /**
-    Validator rule that checks for missing "Required by MIAME" annotation. 
+    Validator rule that checks for missing "Required for MIAME" annotation. 
     Default severity level is ERROR.
   */
   public static final Validator MISSING_MIAME_ANNOTATION = new Validator(
-      "missing.miameannotation", "Missing annotation value", 
-      "Checks if an annotation value has been specified for a 'Required by MIAME' annotation type",
-      "Missing annotation value", Severity.ERROR
-    );
-
+      "missing.miameannotation", "Missing MIAME annotation value", 
+      "Checks if an annotation value has been specified for a 'Required for MIAME' annotation type",
+      "Missing MIAME annotation value", Severity.ERROR
+    );
+
+  /**
+    Validator rule that checks for denied access to an annotation type. 
+    Default severity level is WARNING.
+  */
+  public static final Validator DENIED_ANNOTATIONTYPE = new Validator(
+      "denied.annotationtype", "Access denied to annotation type", 
+      "Checks if the user is denied access to an annotation type",
+      "Access denied to annotation type", Severity.WARNING
+    );
+  
+  /**
+    Validator rule that checks if an item uses a different protocol than
+    specified by the project default. Default severity level is WARNING.
+  */
+  public static final Validator NONDEFAULT_PROTOCOL = new Validator(
+      "nondefault.protocol", "Use of non-default protocol",
+      "Checks if an item uses a different protocol than the default for the current project",
+      "Use of non-default protocol", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks if an item uses a different hardware than
+    specified by the project default. Default severity level is WARNING.
+  */
+  public static final Validator NONDEFAULT_HARDWARE = new Validator(
+      "nondefault.hardware", "Use of non-default hardware",
+      "Checks if an item uses a different hardware (scanner, print robot, etc.) " +
+      "than the default for the current project",
+      "Use of non-default hardware", Severity.WARNING
+    );
+  
+  /**
+    Validator rule that checks if an item uses a different software than
+    specified by the project default. Default severity level is WARNING.
+  */
+  public static final Validator NONDEFAULT_SOFTWARE = new Validator(
+      "nondefault.software", "Use of non-default software",
+      "Checks if an item uses a different software (feature extraction) " +
+      "than the default for the current project",
+      "Use of non-default software", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks if an item uses a different array design than
+    specified by the project default. Default severity level is WARNING.
+  */
+  public static final Validator NONDEFAULT_ARRAYDESIGN = new Validator(
+      "nondefault.arraydesign", "Use of non-default array design",
+      "Checks if an item uses a different array design " +
+      "than the default for the current project",
+      "Use of non-default array design", Severity.WARNING
+    );
+  
+  /**
+    Validator rule that checks if an item uses a different raw data type than
+    specified by the project default. Default severity level is WARNING.
+  */
+  public static final Validator NONDEFAULT_RAWDATATYPE = new Validator(
+      "nondefault.rawdatatype", "Use of non-default raw data type",
+      "Checks if an experiment uses the same raw data type as specified by the " +
+      "default for the current project",
+      "Use of non-default raw data type", Severity.WARNING
+    );
+  
+  /**
+    Validator rule that checks if all raw bioassays in an experiment
+    uses the same array design. Default severity level is WARNING.
+  */
+  public static final Validator MULTIPLE_ARRAYDESIGNS = new Validator(
+      "misc.multiplearraydesigns", "Multiple array designs",
+      "Checks if all raw bioassays in an experiment uses the same " +
+      "array design.",
+      "Multiple array designs", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks if the array design for a raw bioassay
+    matches the array design of the associated hybridization.
+    Default severity level is WARNING.
+  */
+  public static final Validator NONMATHCING_ARRAYDESIGN = new Validator(
+      "misc.nonmatchingarraydesigns", "Array design mismatch",
+      "Checks if the array design for a raw bioassay is the same " +
+      "array design as of the associated hybridization.",
+      "Array design mismatch", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks if the protocol attached to an item
+    has a correct protocol type. Default severity level is WARNING.
+  */
+  public static final Validator INCORRECT_PROTOCOLTYPE = new Validator(
+      "misc.incorrectprotocoltype", "Incorrect protocol type",
+      "Checks if the protocol attached to an item has a correct protocol type.",
+      "Incorrect protocol type", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks if the software attached to an item
+    has a correct software type. Default severity level is WARNING.
+  */
+  public static final Validator INCORRECT_SOFTWARETYPE = new Validator(
+      "misc.incorrectsoftwaretype", "Incorrect software type",
+      "Checks if the software attached to an item has a correct software type.",
+      "Incorrect software type", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks if the hardware attached to an item
+    has a correct hardware type. Default severity level is WARNING.
+  */
+  public static final Validator INCORRECT_HARDWARETYPE = new Validator(
+      "misc.incorrecthardwaretype", "Incorrect hardware type",
+      "Checks if the hardware attached to an item has a correct hardware type.",
+      "Incorrect hardware type", Severity.WARNING
+    );
+  
+  /**
+    Validator rule that checks if the number of labeled extracts
+    attached to a hybridization matches the number of channels in the
+    experiment. Default severity level is ERROR.
+  */
+  public static final Validator INCORRECT_NUM_LABELEDEXTRACTS = new Validator(
+      "misc.incorrectnumlabeledextracts", "Incorrect number of labeled extracts",
+      "Checks if the the number of labeled extracts attached to a hybridzation matches " +
+      "the number of channels in the experiment.",
+      "Incorrect number of labeled extracts", Severity.ERROR
+    );
+  
+  /**
+    Validator rule that checks if a hybridization has more than one
+    labeled extract with the same label. Default severity level is WARNING.
+  */
+  public static final Validator NONUNIQUE_LABEL = new Validator(
+      "misc.nonuniquelabel", "Multiple labeled extracts with same label",
+      "Checks if a hybridization has more than one labeled extract with the same label",
+      "Multiple labeled extracts with same label", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks if a parent to a pooled labeled extract has the
+    same lebel. Default severity level is WARNING.
+  */
+  public static final Validator DIFFERENT_LABEL = new Validator(
+      "misc.differentlabel", "Labeled extract with different label",
+      "Checks if the sources to a pooled labeled extract has the same " +
+      "label as the product",
+      "Labeled extract with different label", Severity.WARNING
+    );
+  
+  /**
+    Validator rule that checks if two items of the same type has the same
+    name. Default severity level is ERROR.
+  */
+  public static final Validator NONUNIQUE_NAME_FOR_TYPE = new Validator(
+      "misc.nonuniquenamefortype", "Non-unique name",
+      "Checks if more than one item of the same type has the same name.",
+      "Non-unique name", Severity.ERROR
+    );
+
+  /**
+    Validator rule that checks if two items of different type has the same
+    name. Default severity level is IGNORE.
+  */
+  public static final Validator NONUNIQUE_NAME_GLOBAL = new Validator(
+      "misc.nonuniquenameglobal", "Global non-unique name",
+      "Checks if more than one item (of any type) has the same name.",
+      "Global non-unique name", Severity.IGNORE
+    );
+
+  /**
+    Validator rule that checks for circular references among pooled items. 
+    Default severity level is ERROR.
+  */
+  public static final Validator CIRCULAR_REFERENCE = new Validator(
+      "misc.circular", "Circular reference to pooled item",
+      "Checks if there are circular references among pooled items.",
+      "Circular reference to pooled item", Severity.ERROR
+    );
+
+  
+  /**
+    Validator rule that checks if an annotation is a protocol parameter.
+    Default severity level is WARNING.
+  */
+  public static final Validator ANNOTATION_IS_PARAMETER = new Validator(
+      "annotation.isparameter", "Annotation is protocol parameter",
+      "Checks if an item has annotations that are protocol parameters.",
+      "Annotation is protocol parameter", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks if an annotation is not valid for the
+    current item type. Default severity level is WARNING.
+  */
+  public static final Validator ANNOTATION_INVALID_ITEM = new Validator(
+      "annotation.invaliditem", "Annotation invalid for item",
+      "Checks if an annotation is invalid for the type of item.",
+      "Annotation is invalid for item", Severity.WARNING
+    );
+
+  /**
+    Validator rule that checks if an annotation value is invalid
+    according to annotation type specification. Default severity level is ERROR.
+  */
+  public static final Validator ANNOTATION_INVALID_VALUE = new Validator(
+      "annotation.invalidvalue", "Annotation has invalid value",
+      "Checks if an annotation has an invalid value.",
+      "Annotation has invalid value", Severity.ERROR
+    );
+  
+  /**
+    Validator rule that checks if an inherited annotation value is inherited
+    from a parent item. Default severity level is ERROR.
+  */
+  public static final Validator ANNOTATION_INHERIT_FROM_NONPARENT = new Validator(
+      "annotation.inhertitfromnonparent", "Inheriting annotation from non-parent",
+      "Checks if an item inherits an annotation that is is not from a parent item.",
+      "Inherting annotation from non-parent", Severity.ERROR
+    );
+  
+  /**
+    Validator rule that checks if two or more inherited annotations have the
+    same annotation type. Default severity level is ERROR.
+  */
+  public static final Validator ANNOTATION_INHERIT_MULTIPLE = new Validator(
+      "annotation.inhertitmultiple", "Inheriting multiple annotation of same type",
+      "Checks if an item inherits more than one annotation of the same annotation type.",
+      "Inheriting multiple annotation of same type", Severity.ERROR
+    );
   
   private String id;

trunk/www/common/annotations/inherit.jsp

@@ -155 +155 @@
 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 DbControl dc = sc.newDbControl();
@@ -169 +170 @@
     loadParents(parentAnnotations, parentItems, item);
   }
-  
+  if (standalone)
+  {
+    sc.getCurrentContext(itemType).setObject("item", item); 
+  }
+  String title = "Inherit annotations to " + 
+    HTML.encodeTags((item instanceof Nameable ? ((Nameable)item).getName() : 
+    (item == null ? " new item" : item.toString())));
+
   // Parent items may have been submitted by caller
   String[] parents = request.getParameterValues("parents");
@@ -317 +325 @@
     event.cancelBubble = true;
   }
+  
+  function saveAnnotations()
+  {
+    var frm = document.forms['modified'];
+    Annotations.addInheritedAnnotationsToForm(window, frm);
+    frm.submit();
+  }
 
   </script>
   </base:head>
-  <base:body onload="init()" style="background: #E0E0E0;">
+  <base:body onload="init()" style="<%=standalone ? "" : "background: #E0E0E0;"%>">
+    <%
+    if (standalone)
+    {
+      %>
+      <h3 class="docked"><%=title%> <base:help helpid="annotations.inherit" /></h3>
+      <div class="boxed" style="background: #E0E0E0">
+      <%
+    }
+    %>
 
   <form name="annotations">
@@ -347 +371 @@
   </tr>
   </table>
-      
   </form>
+
+    <%
+    if (standalone)
+    {
+      %>
+      </div>
+      <table align="center">
+      <tr>
+        <td width="50%"><base:button onclick="saveAnnotations()" title="Save" /></td>
+        <td width="50%"><base:button onclick="window.close()" title="Cancel" /></td>
+      </tr>
+      </table>
+      <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>
+      <%
+    }
+    %>
   </base:body>
   </base:page>

trunk/www/filemanager/directories/list_directories.jsp

@@ -226 +226 @@
     %>
     <base:body onload="initialise()" 
-      style="background: #E0E0E0; border: 1px solid #666666; border-bottom: 0px; padding-left: 0px; padding-right: 0px;" >
+      style="border: 1px solid #999999; border-bottom: 0px; border-right: 0px; padding-left: 0px; padding-right: 0px;" >
     <div id="main" class="joust" style="width:100%;">
       <div id="joust" style="overflow: auto;">

trunk/www/filemanager/files/list_files.jsp

@@ -286 +286 @@
   </base:head>
   
-  <base:body style="border-left: 1px solid #666666; padding-left: 0px; padding-right: 0px;">
+  <base:body style="padding-left: 0px; padding-right: 0px;">
   <m:menu 
     id="move"

trunk/www/filemanager/frameset.jsp

@@ -65 +65 @@
 <base:page type="frameset" title="">
   <base:head />
-  <frameset cols="170,*" frameborder="yes" border="3" >
+  <frameset cols="170,*" frameborder="yes" border="5" >
       <frame name="directories" 
         src="directories/list_directories.jsp?ID=<%=ID%>&mode=<%=mode%>" 
-        scrolling="auto" marginwidth="0" marginheight="0" frameborder="0">
+        scrolling="auto" marginwidth="0" marginheight="0" frameborder="1">
     <frame name="files" 
       src="<%=fileSrc%>"
-      scrolling="auto" marginwidth="0" marginheight="0" frameborder="0">
+      scrolling="auto" marginwidth="0" marginheight="0" frameborder="1">
   </frameset>
 </base:page>

trunk/www/filemanager/manager.jsp

@@ -83 +83 @@
   <iframe name="manager" id="idManager" src="frameset.jsp?ID=<%=ID%>&file_id=<%=fileId%>" width="100%" 
     frameborder="0" vspace="0" hspace="0"
-    marginwidth="0" marginheight="0" scrolling="no" style="overflow: visible"></iframe>
+    marginwidth="0" marginheight="0" scrolling="no" 
+    style="overflow: visible"></iframe>
 </base:body>
 </base:page>

trunk/www/include/scripts/newjoust.js

@@ -194 +194 @@
     @param menuItemIndex The index of the menu item to open
   */
-  this.open = function(menuItemIndex)
+  this.open = function(menuItemIndex, noParents)
   {
     var menuItem = this.menuItems[menuItemIndex];
-    if (!menuItem || menuItem.isOpen) return;
+    if (!menuItem || (menuItem.isOpen && noParents)) return;
     menuItem.isOpen = true;
     Main.show('children'+menuItem.index);
     this.updateIconsAndText(menuItemIndex);
-    if (menuItem.parentItemIndex != -1) this.open(menuItem.parentItemIndex);
+    if (!noParents && menuItem.parentItemIndex != -1) this.open(menuItem.parentItemIndex, false);
   }
   
@@ -211 +211 @@
     for (var i = 0; i < this.menuItems.length; i++)
     {
-      this.open(i);
+      this.open(i, true);
     }
   }
@@ -249 +249 @@
     var menuItem = this.menuItems[menuItemIndex];
     if (!menuItem) return;
-    
+
     if (menuItem.parentItemIndex != -1) this.open(menuItem.parentItemIndex);
     if (menuItemIndex != this.selectedItemIndex)

trunk/www/include/styles/main.css

@@ -332 +332 @@
   border: 0px;
 }
+
+.postit {
+  position: absolute; 
+  width: 200px; 
+  background: #ffffd8; 
+  border: 1px solid #999999;
+  padding: 2px;
+}

trunk/www/include/styles/newjoust.css

@@ -33 +33 @@
 
 .joust .menuitem.hover {
-  background: #F0F0F0;
+  background: #E0E0E0;
   cursor: pointer;
 }

trunk/www/views/experiments/overview/failures.jsp

@@ -95 +95 @@
     else
     {
-      var joust = window.parent.frames['tree'].JoustMenu;
-      var node = joust.menuItems[nodeId]; 
-      joust.select(node.index);
+      window.parent.frames['tree'].selectNode(nodeId);
       if (selectedFailure) Main.removeClass(selectedFailure, 'selected');
       selectedFailure = document.getElementById(failureId);
       Main.addClass(selectedFailure, 'selected');
     }
-  }
-  function validationOptionsOnClick()
-  {
-    Main.openPopup('options.jsp?ID=<%=ID%>', 'ValidationOptions', 700, 500);
-  }
-  function refreshTree()
-  {
-    window.parent.frames['tree'].refreshIfOutdated();
   }
   function itemOnClick(evt, itemType, itemId)
@@ -118 +108 @@
   </base:head>
 
-    <base:body
-      style="background: #E0E0E0;" onload="refreshTree()">
-      <div style="border-bottom: 1px solid #ffffff">
-      <div style="border-bottom: 1px solid #999999">
-        <table>
-        <tr>
-        <td>
-          <b>
-          <%=errors.size() %> error(s);
-          <%=warnings.size()%> warning(s)
-          </b>
-        </td>
-        <td>
-          <base:button onclick="validationOptionsOnClick()" 
-            title="Validation options&hellip;"></base:button>
-        </td>
-        </tr>
-        </table>
-      </div>
+    <base:body>
+      <div style="border-bottom: 1px solid #999999; padding-bottom: 2px;">
+        <b>
+        <%=errors.size() %> error(s),
+        <%=warnings.size()%> warning(s)
+        </b>
       </div>
       
@@ -177 +154 @@
             "error.gif" : "warning.gif"%>" /></td>
             <td class="text" style="border-bottom: 1px dotted #999999; padding: 2px;"
-              ><%=HTML.encodeTags(validator.getFailureSummary() + ": " + node.getTitle()) %>
+              ><%=HTML.encodeTags(failure.getMessage()) %>
+            </td>
+            <td class="text" style="border-bottom: 1px dotted #999999; padding: 2px;"
+              ><%=HTML.encodeTags(node.getTitle()) %>
             </td>
           </tr>

trunk/www/views/experiments/overview/frameset.jsp

@@ -47 +47 @@
     <frame name="tree" 
       src="tree.jsp?ID=<%=ID%>" 
-      scrolling="auto" marginwidth="0" marginheight="0" frameborder="1"
+      scrolling="auto" marginwidth="0" marginheight="4" frameborder="1"
     >
     <frameset rows="*,200" framborder="yes" border="5">
       <frame name="info" 
-        src=""
-        scrolling="auto" marginwidth="0" marginheight="0" frameborder="1"
+        src="info.jsp?ID=<%=ID%>"
+        scrolling="auto" marginwidth="0" marginheight="4" frameborder="1"
       >
       <frame name="failures"
         src="failures.jsp?ID=<%=ID%>"
-        scrolling="auto" marginwidth="0" marginheight="0" frameborder="1"
+        scrolling="auto" marginwidth="0" marginheight="4" frameborder="1"
       >
     </frameset>

trunk/www/views/experiments/overview/index.jsp

@@ -62 +62 @@
   {
     // Display the overview page
-//    Base.getAndSetCurrentContext(sc, itemType, null, defaultContext, true);
     dc = sc.newDbControl();
     Experiment experiment = Experiment.getById(dc, itemId);
     Project project = sc.getActiveProjectId() == 0 ? null : Project.getById(dc, sc.getActiveProjectId());
     ExperimentOverview overview = ExperimentOverview.getOverview(experiment, project);
+    if (Values.getBoolean(request.getParameter("revalidate")))
+    {
+      overview.reset(dc);
+    }
     dc.close();
     forward = "overview.jsp";

trunk/www/views/experiments/overview/options.jsp

@@ -90 +90 @@
     }
   }
+  function setAllInGroup(grpId, severity)
+  {
+    var vldId = 1;
+    var vld = document.getElementById('select.'+grpId+'.'+vldId);
+    while (vld)
+    {
+      for (var i = 0; i < vld.length; i++)
+      {
+        if (vld[i].value == severity) 
+        {
+          vld.selectedIndex = i;
+          i = vld.length;
+        }
+      }
+      vldId++;
+      vld = document.getElementById('select.'+grpId+'.'+vldId);
+    }
+  }
+  function setAllOnChange(grpId, selectList)
+  {
+    var severity = selectList[selectList.selectedIndex].value;
+    selectList.selectedIndex = 0;
+    setAllInGroup(grpId, severity);
+  }
+  
+  function showDescription(evt, validatorId)
+  {
+    var description = 'description.'+validatorId;
+    Main.show(description);
+    var el = document.getElementById(description);
+    el.style.left = (evt.clientX + 10) + 'px';
+    el.style.top = (evt.clientY - 10) + 'px';
+  }
+  function hideDescription(validatorId)
+  {
+    var description = 'description.'+validatorId;
+    Main.hide(description);
+  }
   </script>
   </base:head>
@@ -101 +139 @@
     <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*370)+"px;"%>" 
       position="bottom">
-    <t:tab id="options" title="Validation options" helpid="overview.validationoptions">
+    <t:tab id="options" title="Validation options" helpid="experiment.overview.validationoptions">
     
       <table border="0" cellspacing="0" cellpadding="0">
       <%
       int grp = 0;
+      StringBuilder descriptions = new StringBuilder();
       for (Map.Entry<String, List<Validator>> entry : validators.entrySet())
       {
@@ -113 +152 @@
         %>
         <tr id="grp.<%=grp%>">
-          <td colspan="2"><a href="javascript:toggle(<%=grp%>)"
+          <td style="padding-top: 6px;"><a href="javascript:toggle(<%=grp%>)"
             ><base:icon id="<%="grp."+grp+".icon"%>" 
               image="<%=grp > 1 ? "joust/plusonly.gif" : "joust/minustop.gif"%>" 
-            />&nbsp;<b><%=HTML.encodeTags(title)%></b></a>
+            />&nbsp;<b><%=HTML.encodeTags(title)%></b></a>&nbsp;&nbsp;
+          </td>
+          <td style="padding-top: 6px;">
+            <select name="setall.<%=grp%>" onchange="setAllOnChange(<%=grp%>, this)">
+            <option value="">- set all in this group -
+            <%
+            for (Severity s : Severity.values())
+            {
+              %>
+              <option value="<%=s.name()%>"><%=s%>
+              <%
+            }
+            %>
           </td>
         </tr>
@@ -128 +179 @@
           String validatorId = validator.getId();
           boolean hasNext = vi.hasNext();
+          descriptions.append("<div id=\"description.").append(validatorId).append("\"");
+          descriptions.append(" class=\"postit\" style=\"display:none;\">");
+          descriptions.append(HTML.encodeTags(validator.getDescription()));
+          descriptions.append("</div>\n");
           %>
-          <tr id="vld.<%=grp%>.<%=vld%>" style="<%=grp > 1 ? "display: none;" : ""%>">
-            <td
-              title="<%=HTML.encodeTags(validator.getDescription())%>"
-              ><base:icon image="<%=hasNext ? "joust/big/join.gif" : "joust/big/joinbottom.gif"%>" 
-            /><%=HTML.encodeTags(validator.getTitle())%>&nbsp;&nbsp;</td>
+          <tr id="vld.<%=grp%>.<%=vld%>" style="<%=grp > 1 ? "display: none;" : ""%>"
+            onmouseover="showDescription(event, '<%=validatorId%>')"
+            onmouseout="hideDescription('<%=validatorId%>')"
+            >
+            <td><base:icon 
+              image="<%=hasNext ? "joust/big/join.gif" : "joust/big/joinbottom.gif"%>" 
+              /><%=HTML.encodeTags(validator.getTitle())%>&nbsp;&nbsp;</td>
             <td>
-            <select name="<%=validatorId%>">
+            <select id="select.<%=grp%>.<%=vld%>" name="<%=validatorId%>">
               <%
               for (Severity s : Severity.values())
@@ -152 +209 @@
       %>
       </table>
+      <%=descriptions.toString()%>  
     </t:tab>
     </t:tabcontrol>

trunk/www/views/experiments/overview/overview.jsp

@@ -39 +39 @@
 <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
 <%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
+<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
 <%!
   private static final Item itemType = Item.EXPERIMENT;
@@ -53 +54 @@
   %>
   <base:page title="">
-  <base:head scripts="tabcontrol.js" styles="headertabcontrol.css,path.css">
+  <base:head scripts="tabcontrol.js" styles="toolbar.css,headertabcontrol.css,path.css">
     <script language="JavaScript">
     var timer = 0;
@@ -78 +79 @@
       var iframe = window.frames['overview'];
       var tree = iframe.frames['tree'].document.getElementById('main');
-      if (tree) tree.style.height = (iframeElement.height-1)+'px';
+      if (tree) tree.style.height = (iframeElement.height-8)+'px';
       var joust = iframe.frames['tree'].document.getElementById('joust');
-      if (joust) joust.style.height = (iframeElement.height-1-30)+'px';
+      if (joust) joust.style.height = (iframeElement.height-8)+'px';
       var info = iframe.frames['info'].document.getElementById('main');
       if (info) info.style.height = iframeElement.height+'px';
@@ -114 +115 @@
       }
     }
+    
+    function expandAll()
+    {
+      frames['overview']['tree'].openAll();
+    }
+    function collapseAll()
+    {
+      frames['overview']['tree'].closeAll();
+    }
+    function revalidate()
+    {
+      location.href = 'index.jsp?ID=<%=ID%>&cmd=Overview&revalidate=1';
+    }
+    function validationOptions()
+    {
+      Main.openPopup('options.jsp?ID=<%=ID%>', 'ValidationOptions', 700, 500);
+    }
     </script>
   </base:head>
@@ -127 +145 @@
     <t:tab id="bioassaysets" title="Bioassay sets" />
     <t:tab id="overview" title="Overview">
+    
+      <tbl:toolbar>
+        <tbl:button image="joust/plusonly.gif" title="Expand all"
+          onclick="expandAll()" tooltip="Expand entire tree"/>
+        <tbl:button image="joust/minusonly.gif" title="Collapse all" 
+          onclick="collapseAll()" tooltip="Collapse entire tree" />
+        <tbl:button image="refresh.gif" title="Revalidate" 
+          onclick="revalidate()" tooltip="Revalidate the experiment" />
+        <tbl:button image="configure.png" title="Validation options&hellip;" 
+          onclick="validationOptions()" tooltip="Change validation options" />
+        <tbl:button image="help.gif" title="Help&hellip;"
+          onclick="<%="Main.openHelp('" + ID +"', 'experiment.overview')"%>"
+          tooltip="Get help about this page"
+        />  
+      </tbl:toolbar>
       <iframe name="overview" id="idOverview" src="frameset.jsp?ID=<%=ID%>" width="100%" 
         frameborder="0" vspace="0" hspace="0"
-        marginwidth="0" marginheight="0" scrolling="no" style="overflow: visible"></iframe>
+        marginwidth="0" marginheight="0" scrolling="no" 
+        style="border: 1px solid #999999; border-top: 0px; overflow: visible"></iframe>
     </t:tab>
     </t:tabcontrol>

trunk/www/views/experiments/overview/tree.jsp

@@ -71 +71 @@
       folderIcon += "ChildWarning";
     }
-    if (child.getNodeType() == Node.Type.ITEM && child.getItem() == null)
-    {
-      folderIcon = "ItemDenied";
-    }
     String tooltip = "";
     if (warnings > 0 && errors > 0)
@@ -109 +105 @@
     sb.append(",'").append(HTML.javaScriptEncode(child.getTitle()));
     sb.append(child.getNodeType() == Node.Type.FOLDER ? " (" + numChildren + ")" : "").append("',");
-    sb.append("'','" + HTML.javaScriptEncode(tooltip) + "', '").append(child.getId()).append("')\n");
+    sb.append("'showInfo(\"").append(child.getId()).append("\")','").append(HTML.javaScriptEncode(tooltip)).append("', '").append(child.getId()).append("')\n");
     sb.append(generateSubTree(child, ID));
   }
@@ -168 +164 @@
     IconStore.addIcon('ItemChildError', path + 'itemchilderror.gif', 18, 16);
     IconStore.addIcon('ItemChildErrorSelected', path + 'itemchilderrorselected.gif', 18, 16);
-    IconStore.addIcon('ItemDenied', path + 'itemdenied.gif', 18, 16);
-    IconStore.addIcon('ItemDeniedSelected', path + 'itemdeniedselected.gif', 18, 16);
-    var node<%=rootNode.hashCode()%> = JoustMenu.addMenuItem(-1, '<%=rootIcon%>', '<%=HTML.javaScriptEncode(experiment.getName())%>', '', '', '<%=rootNode.getId()%>');
+    var node<%=rootNode.hashCode()%> = JoustMenu.addMenuItem(-1, '<%=rootIcon%>', '<%=HTML.javaScriptEncode(experiment.getName())%>', 'showInfo("<%=rootNode.getId()%>")', '', '<%=rootNode.getId()%>');
     <%=generateSubTree(rootNode, ID)%>
+    JoustMenu.menuItems[node<%=rootNode.hashCode()%>].isOpen = true;
     JoustMenu.draw('joust');
     isInitialised = true;
@@ -185 +180 @@
     JoustMenu.closeAll();
   }
+  
+  function showInfo(nodeId)
+  {
+    parent.frames['info'].location.href = 'info.jsp?ID=<%=ID%>&nodeId='+nodeId;
+  }
+  
+  function selectNode(nodeId)
+  {
+    var node = JoustMenu.menuItems[nodeId];
+    JoustMenu.select(node.index);
+  }
+  
   var loadedTime = new Date().getTime();
   function refreshIfOutdated()
@@ -196 +203 @@
   </script>
   </base:head>
-    <base:body onload="initialise()" 
-      style="background: #E0E0E0; xborder-right: 1px solid #666666; padding-left: 0px; padding-right: 0px;" >
+    <base:body onload="initialise()">
     <div id="main" class="joust" style="width:100%;">
       <div id="joust" style="overflow: auto;">
       </div>
-      <div style="width:99%;">
-      <table align="center">
-      <tr>
-        <td><base:button onclick="openAll()" title="Expand all" image="joust/plus.gif" /></td>
-        <td><base:button onclick="closeAll()" title="Collapse all" image="joust/minus.gif" /></td>
-      </tr>
-      </table>
-      </div>
     </div>
     </base:body>
-
   </base:page>
   <%