Changeset 7772

Timestamp:

Feb 17, 2020, 8:46:13 AM (22 months ago)

Author:

Nicklas Nordborg

Message:

References #2203: Parent-child transformations should consider the "push annotations" flag

This should now be implemented via the PushToParentsTransformer implementation. Note that this transformer is only added to the first step and move up as long as it finds items that has the "push annotations" flag set.

Location:

trunk/src/core/net/sf/basedb

Files:

• core/query/IdListRestriction.java (modified) (1 diff)
• util/listable/ExtractToParentExtractTransformer.java (modified) (3 diffs)
• util/listable/ExtractToSampleTransformer.java (modified) (2 diffs)
• util/listable/PushToParentsTransformer.java (added)
• util/listable/SampleToBioSourceTransformer.java (modified) (2 diffs)
• util/listable/SampleToParentSampleTransformer.java (modified) (3 diffs)
• util/listable/SourceItemTransformerWithCache.java (modified) (2 diffs)
• util/listable/ToDerivedBioAssaySourceItemTransformerFactory.java (modified) (2 diffs)
• util/listable/ToExtractSourceItemTransformerFactory.java (modified) (2 diffs)
• util/listable/ToPhysicalBioAssaySourceItemTransformerFactory.java (modified) (2 diffs)
• util/listable/ToRawBioAssaySourceItemTransformerFactory.java (modified) (2 diffs)
• util/listable/ToSampleSourceItemTransformerFactory.java (modified) (1 diff)

trunk/src/core/net/sf/basedb/core/query/IdListRestriction.java

@@ -52 +52 @@
   public IdListRestriction(Set<Integer> idList)
   {
-    this.idList = idList;
+    this.idList = new HashSet<>(idList);
     this.idExpression = Hql.property("id");
   }

trunk/src/core/net/sf/basedb/util/listable/ExtractToParentExtractTransformer.java

@@ -48 +48 @@
   private final boolean includeSourcesInTarget;
   private CollectExtracts collectedExtracts;
+  private boolean pushOnly;
   
   /**
@@ -57 +58 @@
     super(Item.EXTRACT, Item.EXTRACT);
     this.includeSourcesInTarget = includeSourcesInTarget;
+  }
+  
+  /**
+    Create a new extract to parent extract transformer that only load parents
+    to extracts that has a subtype with "push annotations" set. This functionality
+    should only be used in the first transformation step.
+    @see PushToParentsTransformer
+    @since 3.16
+  */
+  public ExtractToParentExtractTransformer(boolean includeSourcesInTarget, boolean childrensThatPushOnly)
+  {
+    this(includeSourcesInTarget);
+    this.pushOnly = childrensThatPushOnly;
   }
   
@@ -87 +101 @@
       )
     );
+    if (pushOnly)
+    {
+      query.join(Hql.innerJoin("bm", "itemSubtype", "st"));
+      query.restrict(Restrictions.eq(Hql.property("st", "pushAnnotations"), Expressions.bool(true)));
+    }
 
     // If we have collected downstream extracts we must

trunk/src/core/net/sf/basedb/util/listable/ExtractToSampleTransformer.java

@@ -47 +47 @@
 {
 
+  private boolean pushOnly;
+  
   public ExtractToSampleTransformer()
   {
     super(Item.EXTRACT, Item.SAMPLE);
+  }
+  
+  /**
+    Create a new extract to sample transformer that only load parent samples
+    to extracts that has a subtype with "push annotations" set. This functionality
+    should only be used in the first transformation step.
+    @see PushToParentsTransformer
+    @since 3.16
+  */
+  public ExtractToSampleTransformer(boolean childrensThatPushOnly)
+  {
+    this();
+    this.pushOnly = childrensThatPushOnly;
   }
   
@@ -68 +83 @@
       )
     );
+    if (pushOnly)
+    {
+      query.join(Hql.innerJoin("ch", "itemSubtype", "st"));
+      query.restrict(Restrictions.eq(Hql.property("st", "pushAnnotations"), Expressions.bool(true)));
+    }
     return safeIdList(context.getDbControl(), query, "extracts", source);
   }

trunk/src/core/net/sf/basedb/util/listable/SampleToBioSourceTransformer.java

@@ -44 +44 @@
 {
 
+  private boolean pushOnly;
+  
   public SampleToBioSourceTransformer()
   {
     super(Item.SAMPLE, Item.BIOSOURCE);
+  }
+  
+  /**
+    Create a new sample to biosource transformer that only load parent biosources
+    to sample that has a subtype with "push annotations" set. This functionality
+    should only be used in the first transformation step.
+    @see PushToParentsTransformer
+    @since 3.16
+  */
+  public SampleToBioSourceTransformer(boolean childrensThatPushOnly)
+  {
+    this();
+    this.pushOnly = childrensThatPushOnly;
   }
   
@@ -65 +80 @@
       )
     );
+    if (pushOnly)
+    {
+      query.join(Hql.innerJoin("ch", "itemSubtype", "st"));
+      query.restrict(Restrictions.eq(Hql.property("st", "pushAnnotations"), Expressions.bool(true)));
+    }
     return safeIdList(context.getDbControl(), query, "samples", source);
   }

trunk/src/core/net/sf/basedb/util/listable/SampleToParentSampleTransformer.java

@@ -47 +47 @@
 
   private final boolean includeSourcesInTarget;
+  private boolean pushOnly;
   
   /**
@@ -57 +58 @@
     this.includeSourcesInTarget = includeSourcesInTarget;
   }
-  
+
+  /**
+    Create a new sample to parent sample transformer that only load parents
+    to samples that has a subtype with "push annotations" set. This functionality
+    should only be used in the first transformation step.
+    @see PushToParentsTransformer
+    @since 3.16
+  */
+  public SampleToParentSampleTransformer(boolean includeSourcesInTarget, boolean childrensThatPushOnly)
+  {
+    this(includeSourcesInTarget);
+    this.pushOnly = childrensThatPushOnly;
+  }
+
   @Override
   public Set<Integer> transform(TransformContext context, Set<Integer> source) 
@@ -74 +88 @@
       )
     );
+    if (pushOnly)
+    {
+      query.join(Hql.innerJoin("bm", "itemSubtype", "st"));
+      query.restrict(Restrictions.eq(Hql.property("st", "pushAnnotations"), Expressions.bool(true)));
+    }
     
     // Keep track of all seen children and parents

trunk/src/core/net/sf/basedb/util/listable/SourceItemTransformerWithCache.java

@@ -22 +22 @@
 package net.sf.basedb.util.listable;
 
+import java.util.Collections;
 import java.util.List;
 import java.util.Set;
@@ -124 +125 @@
         if (cache != null) cache.store(key, target);
       }
-      return target;
+      return Collections.unmodifiableSet(target);
     }
   }

trunk/src/core/net/sf/basedb/util/listable/ToDerivedBioAssaySourceItemTransformerFactory.java

@@ -75 +75 @@
       if (sourceItemType == Item.SAMPLE || stepBySource == Item.SAMPLE)
       {
+        // Expand source selection to parents if the children push annotations upwards
+        if (sourceItemType == Item.SAMPLE) chain.add(new PushToParentsTransformer(sourceItemType));
         // Load child samples including the original samples
         chain.add(new SampleToChildSampleTransformer(true));
@@ -89 +91 @@
           // Collect parent extracts since those are also valid when joining child derived bioassays
           chain.add(collectedExtracts.collectParentsOfSource(false));
+          // Expand source selection to parents if the children push annotations upwards
+          chain.add(new PushToParentsTransformer(sourceItemType));
         }
 

trunk/src/core/net/sf/basedb/util/listable/ToExtractSourceItemTransformerFactory.java

@@ -75 +75 @@
       if (sourceItemType == Item.SAMPLE || stepBySource == Item.SAMPLE)
       {
+        // Expand source selection to parents if the children push annotations upwards
+        if (sourceItemType == Item.SAMPLE) chain.add(new PushToParentsTransformer(sourceItemType));
         // Load child samples and include the source samples
         chain.add(new SampleToChildSampleTransformer(true));
@@ -83 +85 @@
       if (sourceItemType == Item.EXTRACT || stepBySource == Item.EXTRACT)
       {
+        // Expand source selection to parents if the children push annotations upwards
+        if (sourceItemType == Item.EXTRACT) chain.add(new PushToParentsTransformer(sourceItemType));
         // Load child extract and maybe include source extracts
         chain.add(new ExtractToChildExtractTransformer(sourceItemType != Item.EXTRACT));

trunk/src/core/net/sf/basedb/util/listable/ToPhysicalBioAssaySourceItemTransformerFactory.java

@@ -75 +75 @@
       if (sourceItemType == Item.SAMPLE || stepBySource == Item.SAMPLE)
       {
+        // Expand source selection to parents if the children push annotations upwards
+        if (sourceItemType == Item.SAMPLE) chain.add(new PushToParentsTransformer(sourceItemType));
         // Load child samples including the original samples
         chain.add(new SampleToChildSampleTransformer(true));
@@ -83 +85 @@
       if (sourceItemType == Item.EXTRACT || stepBySource == Item.EXTRACT)
       {
+        // Expand source selection to parents if the children push annotations upwards
+        if (sourceItemType == Item.EXTRACT) chain.add(new PushToParentsTransformer(sourceItemType));
         // Load child extract and include the source extracts
         chain.add(new ExtractToChildExtractTransformer(true));

trunk/src/core/net/sf/basedb/util/listable/ToRawBioAssaySourceItemTransformerFactory.java

@@ -74 +74 @@
       if (sourceItemType == Item.SAMPLE || stepBySource == Item.SAMPLE)
       {
+        // Expand source selection to parents if the children push annotations upwards
+        if (sourceItemType == Item.SAMPLE) chain.add(new PushToParentsTransformer(sourceItemType));
         // Load child samples including the original samples
         chain.add(new SampleToChildSampleTransformer(true));
@@ -88 +90 @@
           // Collect parent extracts since those are also valid when joining child derived bioassays
           chain.add(collectedExtracts.collectParentsOfSource(false));
+          // Expand source selection to parents if the children push annotations upwards
+          chain.add(new PushToParentsTransformer(sourceItemType));
         }
         

trunk/src/core/net/sf/basedb/util/listable/ToSampleSourceItemTransformerFactory.java

@@ -75 +75 @@
       if (sourceItemType == Item.SAMPLE || stepBySource == Item.SAMPLE)
       {
+        // Expand source selection to parents if the children push annotations upwards
+        if (sourceItemType == Item.SAMPLE) chain.add(new PushToParentsTransformer(sourceItemType));
         // Load child samples and maybe include source samples
         chain.add(new SampleToChildSampleTransformer(sourceItemType != Item.SAMPLE));