Changeset 2973

Timestamp:

Nov 29, 2006, 10:24:26 AM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #449: Innherit BASE 1 sample annotations to BASE 2 RawBioAssays? during migration

Also added a check for BASE 1 user files directory

Location:

branches/2.1/src/clients/migrate

Files:

• net/sf/basedb/clients/migrate/Migrater.java (modified) (1 diff)
• net/sf/basedb/clients/migrate/RawBioAssayTransfer.java (modified) (5 diffs)
• net/sf/basedb/clients/migrate/UploadFileTransfer.java (modified) (1 diff)
• sql/mysql-migration-queries.sql (modified) (1 diff)

branches/2.1/src/clients/migrate/net/sf/basedb/clients/migrate/Migrater.java

@@ -169 +169 @@
       startTransfer(imageFT, "Image");
       RawBioAssayTransfer rawBioAssayT = new RawBioAssayTransfer(userT,
-          groupT, scanT, arrayTypeT, uploadFT, softwareT);
+          groupT, scanT, arrayTypeT, uploadFT, softwareT, sampleT);
       startTransfer(rawBioAssayT, "RawBioAssay");
       RawBioAssayDataTransfer rawBioAssayDataT = new RawBioAssayDataTransfer(

branches/2.1/src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayTransfer.java

@@ -29 +29 @@
 import net.sf.basedb.core.RawBioAssay;
 import net.sf.basedb.core.RawDataTypes;
+import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.Scan;
+
+import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
@@ -47 +50 @@
   private UploadFileTransfer uploadFT = null;
   private SoftwareTransfer softwareT = null;
+  private SampleTransfer sampleT = null;
 
   /**
@@ -56 +60 @@
   RawBioAssayTransfer(UserTransfer userT, GroupTransfer groupT,
       ScanTransfer scanT, ArrayTypeTransfer arrayTypeT,
-      UploadFileTransfer uploadFT, SoftwareTransfer softwareT)
+      UploadFileTransfer uploadFT, SoftwareTransfer softwareT, SampleTransfer sampleT)
   {
     super(userT, groupT);
@@ -66 +70 @@
       this.arrayTypeT = arrayTypeT;
       this.softwareT = softwareT;
+      this.sampleT = sampleT;
     }
     else
@@ -120 +125 @@
       parseFileHeader(rawBioAssay, fileHeader);
     }
+    
+    // Inherit annotations from sample
+    if (sampleT.isDone())
+    {
+      PreparedStatement ps = prepareStatementFromFile("getCh1SampleForRawBioAssay");
+      ps.setInt(1, rs.getInt(1));
+      ResultSet ss = ps.executeQuery();
+      if (ss.next())
+      {
+        int base1SampleId = ss.getInt(1);
+        if (base1SampleId != 0)
+        {
+          Sample s = sampleT.getSampleById(dc, base1SampleId);
+          if (s.isAnnotated())
+          {
+            rawBioAssay.getAnnotationSet().inheritAnnotationSet(s.getAnnotationSet());
+          }
+        }
+      }
+      ss.close();
+    }
+    
     return rawBioAssay;
   }

branches/2.1/src/clients/migrate/net/sf/basedb/clients/migrate/UploadFileTransfer.java

@@ -99 +99 @@
     imageFileMap = new HashMap<Integer, Integer>();
     rawBioAssayFileMap = new HashMap<Integer, Integer>();
+    if (!new java.io.File(path).exists())
+    {
+      String message = "Path for BASE 1 user files not found: " + path;
+      if (!QUICK_TRANSFER)
+      {
+        log(message);
+      }
+      else
+      {
+        stop("UploadFileTransefer", message);
+      }
+    }
   }
 

branches/2.1/src/clients/migrate/sql/mysql-migration-queries.sql

@@ -1033 +1033 @@
 LIMIT   ?, ?;
 
+/* getCh1SampleForRawBioAssay */
+SELECT s.`id` FROM `Sample` s
+INNER JOIN `Extract` e ON e.`sample` = s.`id`
+INNER JOIN `LabeledExtract` le ON le.`extract` = e.`id`
+INNER JOIN `HybridizedLabeled` hl ON hl.`labeled` = le.`id` AND hl.`channel` = 1
+INNER JOIN `ImageAcquisition` ia ON ia.`hybridization` =  hl.`hybridization`
+INNER JOIN `RawBioAssay` rba ON rba.`imageAcquisition` = ia.`id`
+WHERE rba.`id` = ?;
 
 /* selectRawBioAssaysWithSpotData */