Changeset 5695

Timestamp:

Aug 12, 2011, 9:39:05 AM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1153: Handling short read transcript sequence data

Fixes isUsed() and getUsingItems() method for extract and derived bioassay.

Location:

trunk/src/core

Files:

• common-queries.xml (modified) (2 diffs)
• net/sf/basedb/core/DerivedBioAssay.java (modified) (2 diffs)
• net/sf/basedb/core/Extract.java (modified) (3 diffs)

trunk/src/core/common-queries.xml

@@ -1100 +1100 @@
   </query>
 
+  <query id="GET_DERIVEDBIOASSAYS_FOR_EXTRACT" type="HQL">
+    <sql>
+      SELECT {1}
+      FROM DerivedBioAssayData dba
+      WHERE dba.extract = :extract
+    </sql>
+    <description>
+      A Hibernate query that gets the derived bioassays
+      that are referencing a given extract.
+    </description>
+  </query>
+
+  <query id="GET_RAWBIOASSAYS_FOR_EXTRACT" type="HQL">
+    <sql>
+      SELECT {1}
+      FROM RawBioAssayData rba
+      WHERE rba.parentExtract = :extract
+    </sql>
+    <description>
+      A Hibernate query that gets the raw bioassays
+      that are referencing a given extract.
+    </description>
+  </query>
+
   <query id="COUNT_UNREAD_MESSAGES_FOR_USER" type="HQL">
     <sql>
@@ -1381 +1405 @@
     </description>
   </query>
+
+  <query id="GET_CHILD_DERIVEDBIOASSAYS_FOR_DERIVEDBIOASSAY" type="HQL">
+    <sql>
+      SELECT {1}
+      FROM DerivedBioAssayData dba
+      WHERE dba.parent = :bioAssay
+    </sql>
+    <description>
+      A Hibernate query that gets child derived bioassays
+      created from a specific derived bioassay.
+    </description>
+  </query>
+
 
   <query id="GET_RAWBIOASSAYS_FOR_DERIVEDBIOASSAY" type="HQL">

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

@@ -166 +166 @@
   */
   /**
-    
-   */
+    Get all:
+    <ul>
+    <li>Child derived bioassays
+    <li>Child raw bioassays
+    </ul>
+  */
   @Override
   public Set<ItemProxy> getUsingItems()
   {
     Set<ItemProxy> using = super.getUsingItems();
-    // TODO - part of #1153
+    org.hibernate.Session session = getDbControl().getHibernateSession();
+    
+    // Child derived bioassays
+    org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+      "GET_CHILD_DERIVEDBIOASSAYS_FOR_DERIVEDBIOASSAY", "dba.id");
+      /*
+        SELECT {1}
+        FROM DerivedBioAssayData dba
+        WHERE dba.parent = :bioAssay
+      */
+    query.setEntity("bioAssay", this.getData());
+    addUsingItems(using, Item.DERIVEDBIOASSAY, query);
+
+    // Child raw bioassays
+    query = HibernateUtil.getPredefinedQuery(session, 
+      "GET_RAWBIOASSAYS_FOR_DERIVEDBIOASSAY", "rba.id");
+      /*
+        SELECT {1}
+        FROM RawBioAssayData rba
+        WHERE rba.parentBioAssay = :bioAssay
+      */
+    query.setEntity("bioAssay", this.getData());
+    addUsingItems(using, Item.RAWBIOASSAY, query);
+    
     return using;
   }
@@ -183 +210 @@
     throws BaseException
   {
-    // TODO - part of #1153
-    return super.isUsed();
-  }
-  
-  /**
-    Grant READ persmission to everyone that has read permision
-    on the parent physical bioassay.
-  */
-  @Override
-  void initPermissions(int granted, int denied) 
-    throws BaseException
-  {
-    // TODO Auto-generated method stub
-    super.initPermissions(granted, denied);
+    org.hibernate.Session session = getDbControl().getHibernateSession();
+    boolean used = false;
+    
+    if (!used)
+    {
+      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+        "GET_RAWBIOASSAYS_FOR_DERIVEDBIOASSAY", "count(*)");
+      /*
+        SELECT {1}
+        FROM RawBioAssayData rba
+        WHERE rba.parentBioAssay = :bioAssay
+      */
+      query.setEntity("bioAssay", this.getData());
+      used = HibernateUtil.loadData(Long.class, query) > 0;
+    }
+
+    if (!used)
+    {
+      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+        "GET_CHILD_DERIVEDBIOASSAYS_FOR_DERIVEDBIOASSAY", "count(*)");
+      /*
+        SELECT {1}
+        FROM DerivedBioAssayData dba
+        WHERE dba.parent = :bioAssay
+      */
+      query.setEntity("bioAssay", this.getData());
+      used = HibernateUtil.loadData(Long.class, query) > 0;
+    }
+    
+    return used || super.isUsed();
   }
 

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

@@ -165 +165 @@
     <li>no {@link PhysicalBioAssay}:s has been created from this item
     <li>no {@link Extract}:s has been created from this item
+    <li>no {@link DerivedBioAssay} is referencing this item
+    <li>no {@link RawBioAssay} is referencing this item
     </ul>
   */
   public boolean isUsed()
     throws BaseException
-  {   
-    return super.isUsed();
-  }
+  {
+    org.hibernate.Session session = getDbControl().getHibernateSession();
+    boolean used = false;
+    
+    if (!used)
+    {
+      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+        "GET_DERIVEDBIOASSAYS_FOR_EXTRACT", "count(*)");
+      /*
+        SELECT {1}
+        FROM DerivedBioAssayData dba
+        WHERE dba.extract = :extract
+      */
+      query.setEntity("extract", this.getData());
+      used = HibernateUtil.loadData(Long.class, query) > 0;
+    }
+    
+    if (!used)
+    {
+      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
+        "GET_RAWBIOASSAYS_FOR_EXTRACT", "count(*)");
+      /*
+        SELECT {1}
+        FROM RawBioAssayData rba
+        WHERE rba.parentExtract = :extract
+      */
+      query.setEntity("extract", this.getData());
+      used = HibernateUtil.loadData(Long.class, query) > 0;
+    }
+    
+    return used || super.isUsed();
+  }
+  
   /**
     Get all:
     <ul>
+    <li>Child extracts created from the extract
     <li>{@link PhysicalBioAssay}:s created from this extract
+    <li>{@link DerivedBioAssay}:s referencing the extract
+    <li>{@link RawBioAssay}:s referencing the extract
     <ul>
     @since 2.2
@@ -184 +219 @@
     Set<ItemProxy> using = super.getUsingItems();
     org.hibernate.Session session = getDbControl().getHibernateSession();
+    
+    // Physical bioassays
     org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
       "GET_SOURCEEVENTS_FOR_BIOMATERIAL", "bme.physicalBioAssay.id");
@@ -190 +227 @@
         FROM BioMaterialEventData bme
         JOIN bme.sources src
-        WHERE index(src) = :bioMaterial
+        WHERE src.bioMaterial = :bioMaterial
       */
     query.setEntity("bioMaterial", this.getData());
     addUsingItems(using, Item.PHYSICALBIOASSAY, query);
+    
+    // Derived bioassays
+    query = HibernateUtil.getPredefinedQuery(session, 
+        "GET_DERIVEDBIOASSAYS_FOR_EXTRACT", "dba.id");
+        /*
+          SELECT {1}
+          FROM DerivedBioAssayData dba
+          WHERE dba.extract = :extract
+        */
+    query.setEntity("extract", this.getData());
+    addUsingItems(using, Item.DERIVEDBIOASSAY, query);
+    
+    // Raw bioassays
+    query = HibernateUtil.getPredefinedQuery(session, 
+        "GET_RAWBIOASSAYS_FOR_EXTRACT", "rba.id");
+        /*
+          SELECT {1}
+          FROM RawBioAssayData rba
+          WHERE rba.parentExtract = :extract
+        */
+    query.setEntity("extract", this.getData());
+    addUsingItems(using, Item.RAWBIOASSAY, query);
+    
     return using;
   }