Changeset 8086 for branches/3.19-stable

Timestamp:

Oct 27, 2022, 2:13:24 PM (7 months ago)

Author:

Nicklas Nordborg

Message:

References #2285: Values from items with a "push-to-parent" subtype are not displayed in table list

This should fix the problem when the target item is a sample or extract.

Location:

branches/3.19-stable/src

Files:

• clients/web/net/sf/basedb/clients/web/extensions/list/RelatedItemColumn.java (modified) (1 diff)
• core/net/sf/basedb/util/listable/ExtractToChildExtractTransformer.java (modified) (3 diffs)
• core/net/sf/basedb/util/listable/ListableUtil.java (modified) (3 diffs)
• core/net/sf/basedb/util/listable/SampleToChildSampleTransformer.java (modified) (3 diffs)
• core/net/sf/basedb/util/listable/ToBioSourceSourceItemTransformerFactory.java (modified) (1 diff)
• core/net/sf/basedb/util/listable/ToExtractSourceItemTransformerFactory.java (modified) (4 diffs)
• core/net/sf/basedb/util/listable/ToSampleSourceItemTransformerFactory.java (modified) (3 diffs)

branches/3.19-stable/src/clients/web/net/sf/basedb/clients/web/extensions/list/RelatedItemColumn.java

@@ -146 +146 @@
     if (dc != null)
     {
-      SourceItemTransformerFactory transformerFactory = ListableUtil.getTransformerFactory(spec.targetType);
+      boolean includeChildrenThatPushToParents =  !spec.multiHop && 
+          (spec.getTargetType() == Item.EXTRACT || spec.getTargetType() == Item.SAMPLE) && 
+          spec.getItemSubtype(dc).getPushAnnotations();
+      SourceItemTransformerFactory transformerFactory = ListableUtil.getTransformerFactory(spec.targetType, includeChildrenThatPushToParents);
       SourceItemTransformer tmp = transformerFactory.create(spec.sourceType, spec.direction);
       Restriction targetRestriction = spec.createTargetTypeRestriction(dc);

branches/3.19-stable/src/core/net/sf/basedb/util/listable/ExtractToChildExtractTransformer.java

@@ -47 +47 @@
 
   private final boolean includeSourcesInTarget;
+  private final boolean pushOnly;
   
   /**
@@ -54 +55 @@
   public ExtractToChildExtractTransformer(boolean includeSourcesInTarget) 
   {
+    this(includeSourcesInTarget, false);
+  }
+  /**
+    Create a new extract to child extract transformer that only load children
+    has a subtype with "push annotations" set. 
+    @since 3.19.5
+  */
+  public ExtractToChildExtractTransformer(boolean includeSourcesInTarget, boolean childrensThatPushOnly)
+  {
     super(Item.EXTRACT, Item.EXTRACT);
     this.includeSourcesInTarget = includeSourcesInTarget;
+    this.pushOnly = childrensThatPushOnly;
   }
-  
+
   @Override
   public Set<Integer> transform(TransformContext context, Set<Integer> source) 
@@ -75 +86 @@
         Expressions.parameter("parents")
       ));
+    if (pushOnly)
+    {
+      query.join(Hql.innerJoin("itemSubtype", "st"));
+      query.restrict(Restrictions.eq(Hql.property("st", "pushAnnotations"), Expressions.bool(true)));
+    }
 
     // Keep track of all seen children and parents

branches/3.19-stable/src/core/net/sf/basedb/util/listable/ListableUtil.java

@@ -27 +27 @@
 
 import net.sf.basedb.core.Item;
+import net.sf.basedb.core.ItemSubtype;
 import net.sf.basedb.core.Listable;
 import net.sf.basedb.core.SyncFilter.SourceItemTransform;
@@ -66 +67 @@
   public static SourceItemTransformerFactory getTransformerFactory(Item targetItemType)
   {
+    return getTransformerFactory(targetItemType, false);
+  }
+  
+  /**
+    Create a source item transformer factory that can transform items to the given
+    target item type. If no transformer factory exists, null is returned.
+    The 'includeChildrenThatPushToParent' parameter can be used for transforms
+    that go from child to parent items, when the target is a SAMPLE or EXTRACT.
+    When this flag is set, transformer will also include child items that have
+    a subtype that have the {@link ItemSubtype#getPushAnnotations()} flag enabled
+    in the final result.
+    
+    @since 3.19.5
+  */
+  public static SourceItemTransformerFactory getTransformerFactory(Item targetItemType, boolean includeChildrenThatPushToParent)
+  {
     SourceItemTransformerFactory factory = null;
     if (targetItemType == Item.BIOSOURCE)
@@ -73 +90 @@
     else if (targetItemType == Item.SAMPLE)
     {
-      factory = new ToSampleSourceItemTransformerFactory();
+      factory = new ToSampleSourceItemTransformerFactory(includeChildrenThatPushToParent);
     }
     else if (targetItemType == Item.EXTRACT)
     {
-      factory = new ToExtractSourceItemTransformerFactory();
+      factory = new ToExtractSourceItemTransformerFactory(includeChildrenThatPushToParent);
     }
     else if (targetItemType == Item.PHYSICALBIOASSAY)

branches/3.19-stable/src/core/net/sf/basedb/util/listable/SampleToChildSampleTransformer.java

@@ -48 +48 @@
 
   private final boolean includeSourcesInTarget;
+  private final boolean pushOnly;
   
   /**
@@ -55 +56 @@
   public SampleToChildSampleTransformer(boolean includeSourcesInTarget) 
   {
+    this(includeSourcesInTarget, false);
+  }
+  /**
+    Create a new sample to child sample transformer that only load children that
+    has a subtype with "push annotations" set. 
+    @since 3.19.5
+  */
+  public SampleToChildSampleTransformer(boolean includeSourcesInTarget, boolean childrensThatPushOnly)
+  {
     super(Item.SAMPLE, Item.SAMPLE);
     this.includeSourcesInTarget = includeSourcesInTarget;
+    this.pushOnly = childrensThatPushOnly;
   }
-  
+
   @Override
   public Set<Integer> transform(TransformContext context, Set<Integer> source) 
@@ -76 +87 @@
         Expressions.parameter("parents")
       ));
+    if (pushOnly)
+    {
+      query.join(Hql.innerJoin("itemSubtype", "st"));
+      query.restrict(Restrictions.eq(Hql.property("st", "pushAnnotations"), Expressions.bool(true)));
+    }
 
     // Keep track of all seen children and parents

branches/3.19-stable/src/core/net/sf/basedb/util/listable/ToBioSourceSourceItemTransformerFactory.java

@@ -68 +68 @@
 
       // Use utility function to add transformation up to the extract level
-      ToExtractSourceItemTransformerFactory.childToParentChain(chain, sourceItemType, Item.BIOSOURCE);
+      ToExtractSourceItemTransformerFactory.childToParentChain(chain, sourceItemType, Item.BIOSOURCE, false);
       if (chain.size() > 0) 
       {

branches/3.19-stable/src/core/net/sf/basedb/util/listable/ToExtractSourceItemTransformerFactory.java

@@ -50 +50 @@
     { Item.EXTRACT, Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAY, Item.RAWBIOASSAY };
   
+  private final boolean includeChildrenThatPushToParent;
   
   public ToExtractSourceItemTransformerFactory() 
   {
+    this(false);
+  }
+  
+  public ToExtractSourceItemTransformerFactory(boolean includeChildrenThatPushToParent) 
+  {
     super(Item.EXTRACT, PARENT_TO_CHILD, CHILD_TO_PARENT);
+    this.includeChildrenThatPushToParent = includeChildrenThatPushToParent;
   }
   
@@ -93 +100 @@
     else if (transform == SourceItemTransform.CHILD_TO_PARENT)
     {
-      childToParentChain(chain, sourceItemType, Item.EXTRACT);
+      childToParentChain(chain, sourceItemType, Item.EXTRACT, includeChildrenThatPushToParent);
     }
 
@@ -105 +112 @@
     DERIVEDBIOASSAY, PHYSICALBIOASSAY and EXTRACT
   */
-  static void childToParentChain(List<SourceItemTransformer> chain, Item sourceItemType, Item targetItemType)
+  static void childToParentChain(List<SourceItemTransformer> chain, Item sourceItemType, Item targetItemType, boolean includeChildrenThatPushToParent)
   {
     Item stepBySource = null;
@@ -146 +153 @@
       // Load parent extracts, maybe including the source extracts
       chain.add(new ExtractToParentExtractTransformer(sourceItemType != targetItemType, collectedExtracts));
+      // Also include child extracts that have push-to-parent flag set
+      if (includeChildrenThatPushToParent && targetItemType == Item.EXTRACT)
+      {
+        chain.add(new ExtractToChildExtractTransformer(true, true));
+      }
     }
     

branches/3.19-stable/src/core/net/sf/basedb/util/listable/ToSampleSourceItemTransformerFactory.java

@@ -51 +51 @@
   
   
+  private final boolean includeChildrenThatPushToParent;
+  
   public ToSampleSourceItemTransformerFactory() 
   {
-    super(Item.SAMPLE, PARENT_TO_CHILD, CHILD_TO_PARENT);
+    this(false);
   }
   
-  
+  public ToSampleSourceItemTransformerFactory(boolean includeChildrenThatPushToParent) 
+  {
+    super(Item.SAMPLE, PARENT_TO_CHILD, CHILD_TO_PARENT);
+    this.includeChildrenThatPushToParent = includeChildrenThatPushToParent;
+  }
+
   @Override
   public SourceItemTransformer create(final Item sourceItemType, final SourceItemTransform transform) 
@@ -87 +94 @@
       
       // Use utility function to add transformation up to the extract level
-      ToExtractSourceItemTransformerFactory.childToParentChain(chain, sourceItemType, Item.SAMPLE);
+      ToExtractSourceItemTransformerFactory.childToParentChain(chain, sourceItemType, Item.SAMPLE, false);
       if (chain.size() > 0) 
       {
@@ -99 +106 @@
         // Load parent samples and maybe include source samples
         chain.add(new SampleToParentSampleTransformer(sourceItemType != Item.SAMPLE));
+        // Also include child samples that have push-to-parent flag set
+        if (includeChildrenThatPushToParent)
+        {
+          chain.add(new SampleToChildSampleTransformer(true, true));
+        }
       }
     }