Changeset 6092

Timestamp:

Aug 27, 2012, 11:16:54 AM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #1707: Make it possible for a derived bioassay to have multiple physical bioassays as parents

Fixed the derived bioassay batch importer.

Location:

trunk/src

Files:

• core/net/sf/basedb/core/DerivedBioAssay.java (modified) (4 diffs)
• plugins/core/net/sf/basedb/plugins/batchimport/DerivedBioAssayImporter.java (modified) (6 diffs)
• test/TestDerivedBioAssay.java (modified) (3 diffs)
• test/data/test.batchimport.scans.txt (modified) (1 diff)

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

@@ -34 +34 @@
 import java.util.Set;
 
+import net.sf.basedb.core.Transactional.Action;
 import net.sf.basedb.core.data.ArrayBatchData;
 import net.sf.basedb.core.data.ArrayDesignData;
 import net.sf.basedb.core.data.ArraySlideData;
 import net.sf.basedb.core.data.DerivedBioAssayData;
+import net.sf.basedb.core.data.ExtractData;
 import net.sf.basedb.core.data.HardwareData;
 import net.sf.basedb.core.data.PhysicalBioAssayData;
@@ -263 +265 @@
     return used || super.isUsed();
   }
+  
+  /**
+    Automatically try to assign an extract from parent items at
+    creation time.
+  */
+  @Override
+  void onBeforeCommit(Action action)
+  {
+    super.onBeforeCommit(action);
+    
+    if (action == Action.CREATE && !extractHasBeenSet && !isRoot())
+    {
+      ExtractData extract = null;
+      for (DerivedBioAssayData parent : getData().getParents())
+      {
+        ExtractData e = parent.getExtract();
+        if (extract == null)
+        {
+          extract = e;
+        }
+        else if (e != null && !extract.equals(e))
+        {
+          // Different extracts on different parents --> do not assign
+          extract = null;
+          break;
+        }
+      }
+      if (extract != null) getData().setExtract(extract);
+    }
+    
+  }
 
   /**
@@ -614 +647 @@
   }
   
+  private boolean extractHasBeenSet;
+  
   /**
     Set the extract that is the parent of data in this bioassay. The extract 
@@ -624 +659 @@
     checkPermission(Permission.WRITE);
     if (extract != null) extract.checkPermission(Permission.USE);
+    extractHasBeenSet = true;
     getData().setExtract(extract == null ? null : extract.getData());
   }

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/DerivedBioAssayImporter.java

@@ -30 +30 @@
 import net.sf.basedb.core.Path;
 import net.sf.basedb.core.PathParameterType;
-import net.sf.basedb.core.PermissionDeniedException;
 import net.sf.basedb.core.PhysicalBioAssay;
 import net.sf.basedb.core.Item;
@@ -73 +72 @@
         "type is not specified, the importer will try to guess a parent type from the " +
         "item subtype. Example: \\Parent type\\\n\n" +
-        "NOTE! The parent can't be changed for existing bioassays.",
+        "NOTE! The parent type can't be changed for existing bioassays.",
         optionalColumnMapping
     );
@@ -86 +85 @@
         "Mapping that picks the name or id of the parent item (physical or derived bioassay) " +
         "in the data columns. Example: \\Parent\\\n\n" +
-        "NOTE! The parent can't be changed for existing bioassays.",
+        "NOTE! The importer can only add parents, not replace or remove existing parents.",
         optionalColumnMapping
     );
@@ -312 +311 @@
       parentType = parentSubtype.getMainItemType();
     }
-    
-    DerivedBioAssay bioAssay = null;
-    
-    String nameOrId = parentMapper.getValue(data);
-    if (parentType == Item.DERIVEDBIOASSAY)
-    {
-      DerivedBioAssay parent = findDerivedBioAssay(dc, FallbackIdMethod.NAME_OR_ID, nameOrId, parentSubtype);
-      bioAssay = DerivedBioAssay.getNew(dc, parent, job.getJob());
-    }
-    else
-    {
-      PhysicalBioAssay pba = findPhysicalBioAssay(dc, FallbackIdMethod.NAME_OR_ID, nameOrId, parentSubtype);
-      bioAssay = DerivedBioAssay.getNew(dc, pba, job.getJob());
-    }
-    
+    boolean isRoot = parentType != Item.DERIVEDBIOASSAY;
+    DerivedBioAssay bioAssay = DerivedBioAssay.getNew(dc, isRoot, job.getJob());
+        
     if (subtype != null) bioAssay.setItemSubtype(subtype);
     updateItem(dc, bioAssay, data);
@@ -343 +330 @@
       ItemSubtype type = ItemSubtype.getRelatedSubtype(dc, bioAssay, Item.EXTRACT, 0);
       Extract extract = findExtract(dc, FallbackIdMethod.NAME_OR_EXTERNALID_OR_ID, nameOrId, type);
-      if (extract == null && !bioAssay.isRoot())
-      {
-        // No explicit extract found, try the extract on the parent bioassay
-        try
-        {
-          extract = bioAssay.getParent().getExtract();
-        }
-        catch (PermissionDeniedException ex)
-        {}
-      }
       if (nameOrId == null || extract != null) bioAssay.setExtract(extract);
     }
@@ -410 +387 @@
       }
     }
-  }
+    
+    if (parentMapper != null)
+    {
+      String nameOrId = parentMapper.getValue(data);
+      Item parentType = bioAssay.isRoot() ? Item.PHYSICALBIOASSAY : Item.DERIVEDBIOASSAY;
+      
+      ItemSubtype parentSubtype = ItemSubtype.getRelatedSubtype(dc, bioAssay, parentType);
+      if (parentType == Item.DERIVEDBIOASSAY)
+      {
+        DerivedBioAssay parent = findDerivedBioAssay(dc, FallbackIdMethod.NAME_OR_ID, nameOrId, parentSubtype);
+        bioAssay.addParent(parent);
+      }
+      else
+      {
+        PhysicalBioAssay pba = findPhysicalBioAssay(dc, FallbackIdMethod.NAME_OR_ID, nameOrId, parentSubtype);
+        bioAssay.addPhysicalBioAssay(pba);
+      }
+    }
+  }
+  
   /**
     Validate data files if they have been set.

trunk/src/test/TestDerivedBioAssay.java

@@ -23 +23 @@
 import net.sf.basedb.core.*;
 
+import java.util.ArrayList;
 import java.util.Date;
 import java.util.Set;
@@ -390 +391 @@
     if (!TestUtil.getSilent())
     {
-      write("   \tID \tName      \tType\tDescription\tParent\tPhysical bioassay\tProtocol\tHardware\tSoftware");
-      write("-- \t-- \t--------- \t----\t-----------\t------\t----------------\t---------\t--------\t--------");
+      write("   \tID \tName      \tType\tDescription\tParents\tPhysical bioassays\tProtocol\tHardware\tSoftware");
+      write("-- \t-- \t--------- \t----\t-----------\t-------\t------------------\t--------\t--------\t--------");
     }
   }
@@ -399 +400 @@
     if (!TestUtil.getSilent()) 
     {
+      DbControl dc = dbas.getDbControl();
       System.out.println(i+":\t"+dbas.getId()+"\t"+dbas.getName()+"\t"+dbas.getItemSubtype()+"\t"+dbas.getDescription()+
-        "\t"+dbas.getParent()+"\t"+dbas.getPhysicalBioAssay()+
+        "\t"+new ArrayList<DerivedBioAssay>(dbas.getParents().list(dc))+
+        "\t"+new ArrayList<PhysicalBioAssay>(dbas.getPhysicalBioAssays().list(dc))+
         "\t"+dbas.getProtocol()+"\t"+dbas.getHardware()+"\t"+dbas.getSoftware());
     }

trunk/src/test/data/test.batchimport.scans.txt

@@ -3 +3 @@
 Scan 2  Scan  The second  Hyb 2 Labeled 2.1 Scanning  Scanner
 Scan 3  Scan    Hyb all
-Child bioassay 1  ChildScan A child to Scan 1 Scan 1  
+Child bioassay 1  ChildScan Merged scans  Scan 1
+Child bioassay 1      Scan 2
+Child bioassay 1      Scan 3